Variant report

Variant	rs7626013
Chromosome Location	chr3:59961159-59961160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:59961121-59961222	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
NPCDR1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1038517	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs10510821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707816	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11708404	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs11715559	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs17031569	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061678	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17061689	1.00[JPT][hapmap]
rs17061708	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17061716	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs212020	1.00[MEX][hapmap]
rs2687898	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736814	1.00[MEX][hapmap]
rs3772460	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3772474	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3772487	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3772489	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3772503	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3772504	1.00[JPT][hapmap]
rs3821484	1.00[JPT][hapmap]
rs58731594	0.89[ASN][1000 genomes]
rs60751140	1.00[ASN][1000 genomes]
rs62240114	0.89[ASN][1000 genomes]
rs72877030	1.00[ASN][1000 genomes]
rs72877033	1.00[ASN][1000 genomes]
rs72877036	1.00[ASN][1000 genomes]
rs974035	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590388	chr3:59957252-60018326	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59943200-59964400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:59952000-59961600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:59952000-59964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:59956200-59964200	Weak transcription	Fetal Thymus	thymus
5	chr3:59957600-59962000	Strong transcription	Dnd41	blood
6	chr3:59959000-59961400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:59959200-59961800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:59959800-59961800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:59960800-59963000	Weak transcription	Primary T cells from cord blood	blood

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