Variant report

Variant	rs7496431
Chromosome Location	chr15:77452054-77452055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1015813	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10162742	0.85[YRI][hapmap]
rs10519158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11853625	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853633	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854182	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854466	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][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];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856538	0.96[CHD][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.90[ASN][1000 genomes]
rs11857330	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11857804	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12900110	0.86[ASN][1000 genomes]
rs12902106	0.83[ASN][1000 genomes]
rs12902434	0.83[ASN][1000 genomes]
rs12902446	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13379686	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13380152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374201	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1446313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs17381652	0.84[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs17381821	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17383078	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17466480	0.91[ASN][1000 genomes]
rs17468413	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1867780	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044453	0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs2137977	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292594	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]
rs2864079	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs35093280	0.89[ASN][1000 genomes]
rs4592615	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4638539	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886514	0.84[ASN][1000 genomes]
rs4886852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886857	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55881066	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55994208	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56070388	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58792939	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59831220	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60079927	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60761381	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60863150	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173670	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74025074	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74025104	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74025105	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74027548	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74027549	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7496431	CRABP1	cis	parietal	SCAN
rs7496431	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs7496431	HMG20A	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77426000-77452400	Weak transcription	Pancreas	Pancrea
2	chr15:77426200-77453200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
4	chr15:77434200-77460400	Weak transcription	Fetal Brain Male	brain
5	chr15:77436000-77457800	Weak transcription	Spleen	Spleen
6	chr15:77437000-77471200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:77437600-77453400	Weak transcription	HMEC	breast
8	chr15:77438000-77453200	Weak transcription	Fetal Heart	heart
9	chr15:77438000-77453400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:77438400-77461000	Weak transcription	NH-A	brain
11	chr15:77438600-77457600	Weak transcription	Gastric	stomach
12	chr15:77438600-77461400	Weak transcription	Aorta	Aorta
13	chr15:77438600-77469000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:77438600-77470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:77439800-77460600	Weak transcription	HSMMtube	muscle
16	chr15:77440200-77453000	Weak transcription	Fetal Kidney	kidney
17	chr15:77444200-77460600	Weak transcription	NHEK	skin
18	chr15:77445200-77461000	Weak transcription	Small Intestine	intestine
19	chr15:77446400-77454600	Weak transcription	Esophagus	oesophagus
20	chr15:77447800-77453800	Weak transcription	K562	blood
21	chr15:77447800-77456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:77448000-77452400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:77448200-77452400	Weak transcription	Fetal Thymus	thymus
24	chr15:77448200-77457400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:77448600-77452400	Weak transcription	Lung	lung
26	chr15:77448800-77452200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:77448800-77452200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:77448800-77453000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr15:77449000-77465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:77449400-77452600	Weak transcription	HepG2	liver
31	chr15:77449600-77453600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:77449800-77453200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:77450000-77452400	Weak transcription	Fetal Stomach	stomach
34	chr15:77450000-77453200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:77450000-77453400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:77450000-77453400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:77450000-77455200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:77450000-77458000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:77450000-77460600	Weak transcription	Left Ventricle	heart
40	chr15:77450200-77453400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr15:77450200-77453400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr15:77450400-77452400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:77450400-77452800	Weak transcription	Colonic Mucosa	Colon
44	chr15:77450400-77453200	Weak transcription	Brain Angular Gyrus	brain
45	chr15:77450400-77471200	Weak transcription	Fetal Muscle Leg	muscle
46	chr15:77450600-77453000	Weak transcription	Liver	Liver
47	chr15:77450600-77471200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:77450800-77452800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:77450800-77453200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:77450800-77453800	Weak transcription	Colon Smooth Muscle	Colon

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