Variant report

Variant	rs2276885
Chromosome Location	chr4:76928729-76928730
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	ZNF217	chr4:76928216-76928757	MCF-7	breast:	n/a	n/a
2	STAT1	chr4:76928457-76928998	Hela-S3	cervix:	n/a	chr4:76928822-76928829
3	GATA3	chr4:76928142-76928742	MCF-7	breast:	n/a	chr4:76928460-76928471

Variant related genes	Relation type
CXCL9	TF binding region
ART3	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10337	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11735706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12648437	0.82[ASN][1000 genomes]
rs12648687	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12651276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17001237	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17001273	0.82[ASN][1000 genomes]
rs2271527	1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs2292534	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2869460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733239	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs3796482	0.82[ASN][1000 genomes]
rs3796483	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs4626230	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs57946262	0.86[ASN][1000 genomes]
rs61487959	0.84[ASN][1000 genomes]
rs66932304	0.83[ASN][1000 genomes]
rs67906710	0.82[ASN][1000 genomes]
rs68181445	0.82[ASN][1000 genomes]
rs6838162	0.84[ASN][1000 genomes]
rs6840076	0.85[ASN][1000 genomes]
rs6841376	0.85[ASN][1000 genomes]
rs6849878	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs72607852	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs868007	1.00[YRI][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2276885	GDEP	cis	cerebellum	SCAN
rs2276885	NUP54	cis	parietal	SCAN
rs2276885	NUP54	cis	Nerve Tibial	GTEx
rs2276885	SCARB2	cis	parietal	SCAN
rs2276885	NUP54	cis	Thyroid	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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