Variant report

Variant	rs2276811
Chromosome Location	chr3:52847984-52847985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52847640..52851112-chr3:52852588..52855076,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13322530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001734	1.00[CHD][hapmap]
rs2256734	1.00[CHD][hapmap]
rs2276813	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276820	1.00[CHD][hapmap]
rs2276821	1.00[CHD][hapmap]
rs2276822	1.00[CHD][hapmap]
rs2336155	1.00[CHD][hapmap]
rs2336559	1.00[CHD][hapmap]
rs2535619	1.00[CHD][hapmap]
rs2535632	1.00[CHD][hapmap]
rs2535637	1.00[CHD][hapmap]
rs2710324	1.00[CHD][hapmap]
rs2710333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2710334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2710335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2710337	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2710338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs28463071	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878633	1.00[CHD][hapmap]
rs3774357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234637	1.00[CHB][hapmap]
rs4687665	1.00[CHD][hapmap]
rs55888310	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58014366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60309163	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6774869	1.00[CHD][hapmap]
rs72954395	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72954399	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72956104	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72956110	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311481	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681089	1.00[CHD][hapmap]
rs9831540	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9861870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52836800-52851600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:52836800-52851800	Weak transcription	Pancreas	Pancrea
3	chr3:52838400-52852000	Weak transcription	Spleen	Spleen
4	chr3:52841600-52850600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:52844000-52854000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:52844200-52856600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:52844400-52857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:52844600-52851600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:52844600-52851800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:52844600-52856800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:52844600-52857600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:52845400-52851200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:52845600-52853000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:52845800-52854200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:52846000-52853200	Weak transcription	Thymus	Thymus
16	chr3:52846200-52849000	Weak transcription	Right Atrium	heart
17	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
18	chr3:52846600-52849000	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:52846800-52848400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:52846800-52857000	Weak transcription	Aorta	Aorta
21	chr3:52847000-52857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:52847200-52848000	Strong transcription	Fetal Muscle Leg	muscle
23	chr3:52847200-52851800	Weak transcription	Fetal Thymus	thymus
24	chr3:52847200-52861200	Genic enhancers	Liver	Liver
25	chr3:52847400-52857000	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
27	chr3:52847800-52848000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:52847800-52850800	Weak transcription	Fetal Stomach	stomach
29	chr3:52847800-52852200	Weak transcription	HepG2	liver
30	chr3:52847800-52854600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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