Variant report

Variant	rs3771274
Chromosome Location	chr2:47663845-47663846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57914771..57917059-chr2:47663022..47665439,2	MCF-7	breast:
2	chr2:47663794..47664989-chr2:47994770..47995591,3	MCF-7	breast:
3	chr2:47663402..47665141-chr2:47994504..47995700,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10175959	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10188090	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10209369	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10495945	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11125136	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11684661	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11684737	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11694689	0.82[EUR][1000 genomes]
rs11886591	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11889077	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712993	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712994	0.82[EUR][1000 genomes]
rs1981927	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981928	0.94[ASN][1000 genomes]
rs2059520	0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2081483	0.87[ASN][1000 genomes]
rs2081484	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2081485	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2162121	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2347794	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2347795	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764960	0.80[ASN][1000 genomes]
rs3771272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771273	0.81[EUR][1000 genomes]
rs3771275	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771276	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771280	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3771281	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821227	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4452202	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4550716	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs4583514	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4596025	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544989	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544990	0.92[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6704794	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6707467	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6711675	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6719539	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6720555	0.89[EUR][1000 genomes]
rs6724382	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6724876	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6726691	0.95[ASN][1000 genomes]
rs6726832	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6729015	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6739590	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741139	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6744097	0.81[JPT][hapmap]
rs6754473	0.87[EUR][1000 genomes]
rs6757035	0.87[ASN][1000 genomes]
rs6758327	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6759990	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs7565513	0.81[ASN][1000 genomes]
rs7575871	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586575	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7593412	0.81[ASN][1000 genomes]
rs7596629	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7599880	0.82[EUR][1000 genomes]
rs7607076	0.96[ASN][1000 genomes]
rs7607312	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs876936	0.84[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap]

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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers 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 miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv527823	chr2:47645249-47709704	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3771274	EPCAM	cis	cerebellum	SCAN
rs3771274	MSH2	cis	cerebellum	SCAN
rs3771274	EPCAM	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47631400-47697000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:47631400-47714400	Weak transcription	Right Ventricle	heart
3	chr2:47631800-47672000	Weak transcription	Pancreas	Pancrea
4	chr2:47631800-47696600	Weak transcription	Esophagus	oesophagus
5	chr2:47631800-47700000	Weak transcription	Colonic Mucosa	Colon
6	chr2:47631800-47704200	Weak transcription	Psoas Muscle	Psoas
7	chr2:47633000-47714000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:47643600-47703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:47644800-47692000	Weak transcription	Fetal Brain Male	brain
10	chr2:47648600-47668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:47652000-47666400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:47655600-47682800	Weak transcription	Stomach Mucosa	stomach
13	chr2:47657800-47664800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:47658000-47670600	Weak transcription	Aorta	Aorta
15	chr2:47658000-47674800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:47658000-47690400	Weak transcription	NHEK	skin
17	chr2:47658000-47707000	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:47658000-47714200	Weak transcription	Small Intestine	intestine
19	chr2:47658200-47665200	Weak transcription	HMEC	breast
20	chr2:47658200-47665200	Weak transcription	K562	blood
21	chr2:47658200-47665400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:47658200-47668800	Weak transcription	Spleen	Spleen
23	chr2:47658200-47670600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:47658200-47671200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:47658200-47673000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:47658200-47674800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:47658200-47690200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:47658200-47690400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:47658200-47690400	Weak transcription	Left Ventricle	heart
30	chr2:47658200-47690600	Weak transcription	Brain Anterior Caudate	brain
31	chr2:47658200-47691000	Weak transcription	Gastric	stomach
32	chr2:47658200-47692600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:47658200-47692600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:47658200-47709200	Weak transcription	Brain Substantia Nigra	brain
35	chr2:47658200-47710400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:47658200-47713400	Weak transcription	Fetal Heart	heart
37	chr2:47658200-47714200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:47658200-47714800	Weak transcription	HSMMtube	muscle
39	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:47658400-47664800	Weak transcription	Primary T cells from cord blood	blood
41	chr2:47658400-47664800	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:47658400-47665000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:47658400-47665000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:47658400-47665200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:47658400-47665200	Weak transcription	Fetal Brain Female	brain
46	chr2:47658400-47666000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:47658400-47670200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:47658400-47672600	Weak transcription	NHDF-Ad	bronchial
49	chr2:47658400-47672800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr2:47658400-47673000	Weak transcription	Liver	Liver

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