Variant report

Variant	rs2292594
Chromosome Location	chr15:77515140-77515141
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	chr15:77496480..77498280-chr15:77514444..77516780,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259722	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1015813	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10162742	0.85[YRI][hapmap]
rs10519158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11853625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853633	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11854182	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11854466	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856538	0.96[CHD][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.83[ASN][1000 genomes]
rs11857330	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11857804	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12148274	0.89[ASN][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900110	0.90[ASN][1000 genomes]
rs12902106	0.93[ASN][1000 genomes]
rs12902434	0.93[ASN][1000 genomes]
rs12902446	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12912963	0.89[ASN][1000 genomes]
rs13379686	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13380152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1374201	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs17381652	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs17381821	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17383078	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17466480	0.84[ASN][1000 genomes]
rs17468413	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867780	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2044453	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs2137977	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2864079	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs35093280	0.82[ASN][1000 genomes]
rs4592615	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4638539	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886514	0.89[ASN][1000 genomes]
rs4886852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886857	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55881066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994208	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56070388	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58792939	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59831220	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60079927	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60761381	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60863150	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173670	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74025074	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74025104	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74025105	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74027548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74027549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7496431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2292594	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs2292594	CRABP1	cis	parietal	SCAN
rs2292594	HMG20A	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77473600-77527800	Weak transcription	Placenta	Placenta
2	chr15:77480400-77528000	Weak transcription	Fetal Stomach	stomach
3	chr15:77482200-77528000	Weak transcription	Spleen	Spleen
4	chr15:77484000-77518800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:77487400-77516800	Weak transcription	Fetal Heart	heart
6	chr15:77492000-77516600	Weak transcription	NH-A	brain
7	chr15:77492000-77517000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:77492200-77516600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:77492200-77516800	Weak transcription	Adipose Nuclei	Adipose
10	chr15:77492200-77516800	Weak transcription	NHLF	lung
11	chr15:77492200-77527400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:77492200-77527800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:77492200-77527800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:77492200-77528200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:77492400-77516600	Weak transcription	Fetal Intestine Small	intestine
16	chr15:77492400-77516800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:77492400-77516800	Weak transcription	Primary B cells from cord blood	blood
18	chr15:77492400-77544000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:77492600-77516600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:77492600-77516800	Weak transcription	Aorta	Aorta
21	chr15:77492800-77516400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:77494600-77516600	Weak transcription	Brain Substantia Nigra	brain
23	chr15:77494800-77518800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:77500000-77515600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:77500400-77515400	Weak transcription	Fetal Lung	lung
26	chr15:77500400-77516000	Weak transcription	Dnd41	blood
27	chr15:77500400-77516800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:77501000-77523000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:77501000-77527400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:77501800-77515400	Weak transcription	Primary T cells from cord blood	blood
31	chr15:77501800-77516000	Weak transcription	HSMM	muscle
32	chr15:77502200-77524800	Weak transcription	Osteobl	bone
33	chr15:77502400-77515800	Weak transcription	HUVEC	blood vessel
34	chr15:77505800-77559400	Weak transcription	Psoas Muscle	Psoas
35	chr15:77507400-77516400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:77507400-77516600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:77507600-77528200	Weak transcription	Left Ventricle	heart
38	chr15:77508000-77543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:77509800-77516000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:77509800-77528000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:77511200-77541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:77511400-77516600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:77512200-77516200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:77512800-77515200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:77512800-77516400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:77512800-77516800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:77513600-77516600	Weak transcription	NHDF-Ad	bronchial
48	chr15:77514200-77517800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr15:77514400-77515200	Weak transcription	Pancreas	Pancrea
50	chr15:77514400-77516800	Weak transcription	Ovary	ovary

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