Variant report

Variant	rs2279965
Chromosome Location	chr4:48076248-48076249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48069308..48072567-chr4:48073439..48077875,4	K562	blood:
2	chr4:48019513..48022096-chr4:48074921..48077158,2	MCF-7	breast:
3	chr4:48074919..48077671-chr4:48081948..48084099,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074966	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1003872	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1003873	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13116684	0.84[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs13150783	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs13151608	0.87[JPT][hapmap]
rs1567217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1911669	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2661528	0.85[TSI][hapmap]
rs2704401	0.85[TSI][hapmap]
rs2940328	0.84[ASN][1000 genomes]
rs321632	0.87[JPT][hapmap]
rs62301688	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279965	JPH1	trans	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48066800-48076400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:48067000-48082000	Strong transcription	Primary T cells from cord blood	blood
3	chr4:48067400-48078600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:48067600-48080400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:48067600-48081200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:48067600-48102400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:48067800-48081600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:48068600-48080000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:48069600-48082600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr4:48069800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:48070800-48105200	Weak transcription	GM12878-XiMat	blood
12	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:48074000-48080600	Weak transcription	Hela-S3	cervix
15	chr4:48074400-48080200	Weak transcription	Placenta	Placenta
16	chr4:48075200-48076600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:48075200-48077000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:48075400-48076600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr4:48075400-48077200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:48075600-48076400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:48075600-48076400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr4:48075600-48076600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr4:48075600-48076800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:48075800-48076600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:48075800-48077000	Weak transcription	Stomach Mucosa	stomach
26	chr4:48075800-48082000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:48076000-48076600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:48076000-48081400	Weak transcription	HMEC	breast
29	chr4:48076200-48080600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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