Variant report

Variant	rs2276886
Chromosome Location	chr4:76928428-76928429
allele	A/G
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	ZNF217	chr4:76928216-76928757	MCF-7	breast:	n/a	n/a
2	JUND	chr4:76928318-76928638	Hela-S3	cervix:	n/a	n/a
3	ARID3A	chr4:76928347-76928470	HepG2	liver:	n/a	n/a
4	NR2F2	chr4:76928170-76928675	MCF-7	breast:	n/a	n/a
5	GATA3	chr4:76928360-76928695	MCF-7	breast:	n/a	chr4:76928460-76928471
6	FOS	chr4:76928340-76928540	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr4:76928325-76928612	HepG2	liver:	n/a	n/a
8	GATA3	chr4:76928142-76928742	MCF-7	breast:	n/a	chr4:76928460-76928471
9	TCF7L2	chr4:76928226-76928578	MCF-7	breast:	n/a	n/a
10	FOSL2	chr4:76928247-76928694	MCF-7	breast:	n/a	n/a
11	GATA3	chr4:76928292-76928613	MCF-7	breast:	n/a	chr4:76928460-76928471
12	FOS	chr4:76928359-76928638	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ART3	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10007919	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10009947	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10021434	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10029157	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10031733	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031983	0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10518143	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12374321	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12374370	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12649185	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13111494	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs13112512	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13118503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13129896	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130917	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1394916	1.00[YRI][hapmap]
rs17001247	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17224545	1.00[LWK][hapmap]
rs1857821	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242470	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271528	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375800	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28422144	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28451731	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28532601	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28535831	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28588114	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28595360	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28647886	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2869462	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34630680	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34740469	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733238	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796484	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241577	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4429750	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859567	0.94[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs4859570	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859571	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4859572	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859573	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859577	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859580	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859609	0.81[CHB][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs55876513	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66498356	0.83[ASN][1000 genomes]
rs6847815	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs884004	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884304	0.83[EUR][1000 genomes]
rs9994667	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2276886	NAAA	cis	cerebellum	SCAN
rs2276886	CXCL11	cis	multi-tissue	Pritchard
rs2276886	NAAA	cis	lymphoblastoid	seeQTL
rs2276886	CXCL10	cis	multi-tissue	Pritchard
rs2276886	NAAA	cis	Whole Blood	GTEx
rs2276886	NAAA	cis	Artery Aorta	GTEx
rs2276886	NAAA	cis	Esophagus Muscularis	GTEx
rs2276886	NAAA	cis	parietal	SCAN
rs2276886	FAM47E	cis	cerebellum	SCAN
rs2276886	CXCL10	cis	lymphoblastoid	seeQTL
rs2276886	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs2276886	RCHY1	cis	cerebellum	SCAN
rs2276886	ASAHL	cis	multi-tissue	Pritchard
rs2276886	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs2276886	NAAA	cis	Esophagus Mucosa	GTEx
rs2276886	CDKL2	cis	parietal	SCAN
rs2276886	NAAA	cis	Muscle Skeletal	GTEx
rs2276886	NAAA	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76912400-76932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76927000-76929200	Enhancers	Fetal Intestine Large	intestine
3	chr4:76927200-76928800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:76927200-76929000	Enhancers	Fetal Intestine Small	intestine
5	chr4:76927600-76929000	Enhancers	HMEC	breast
6	chr4:76927600-76929000	Enhancers	NHEK	skin
7	chr4:76927600-76929200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:76927600-76929200	Enhancers	Liver	Liver
9	chr4:76927800-76928800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:76928200-76928800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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