Frequency is up to 70% on most lines.  JR Joban Line rapid, a line 
already notorious for its rush-hour congestion, is an exception with a 
rush-hour frequency of 60%

The following JR East sections will be closed for some hours:

Tohoku Line north of Utsunomiya.
Kawagoe Line west of Kawagoe and Hachiko Line north of Komagawa.
Sagami Line.
Ito Line.

JR lines in the Bousou area, west and south of Chiba.

Oume Line will be open all day today.

No reports of section closures from non-JR companies for today.

Exact time frames of line closures available here:
http://www46.atwiki.jp/earthquakeinfo_en/pages/15.html