Variant report

Variant	rs6682737
Chromosome Location	chr1:113136229-113136230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113133844..113136355-chr1:113152483..113154108,2	MCF-7	breast:
2	chr1:113133172..113139000-chr1:113157141..113162123,6	K562	blood:
3	chr1:113134544..113137482-chr1:113243651..113245216,2	MCF-7	breast:
4	chr1:113135812..113137373-chr1:113160331..113162478,2	MCF-7	breast:
5	chr1:113134598..113136767-chr1:113161430..113163765,2	K562	blood:
6	chr1:113131312..113132892-chr1:113136156..113138926,2	K562	blood:

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1001494	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1006298	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10745330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10776755	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs10776756	0.86[EUR][1000 genomes]
rs10776757	0.89[CEU][hapmap]
rs10857963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102497	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102512	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584092	0.88[CEU][hapmap]
rs12046208	0.89[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs12046329	0.82[AMR][1000 genomes]
rs12046466	0.83[AMR][1000 genomes]
rs12126277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12728001	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1994604	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932532	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs2932536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999154	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs2999155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs3013439	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3013440	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3103450	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351372	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4838959	0.82[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs4839254	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6537743	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537748	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs6537749	0.82[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs6666579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669096	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679414	0.82[EUR][1000 genomes]
rs6691932	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700673	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7415820	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7513716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7522288	0.82[CEU][hapmap]
rs7524494	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7546094	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554345	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7554916	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902289	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs910697	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9429486	0.89[CEU][hapmap]
rs954679	0.81[JPT][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6682737	ST7L	cis	Esophagus Muscularis	GTEx
rs6682737	ST7L	cis	Stomach	GTEx
rs6682737	WNT2B	cis	parietal	SCAN
rs6682737	ST7L	cis	Heart Left Ventricle	GTEx
rs6682737	ST7L	cis	Adipose Subcutaneous	GTEx
rs6682737	ST7L	cis	Nerve Tibial	GTEx
rs6682737	ST7L	cis	uninvolved skin	skin_eQTL
rs6682737	ST7L	cis	Artery Tibial	GTEx
rs6682737	ST7L	cis	lung	GTEx
rs6682737	ST7L	cis	Lymphoblastoid	GTEx
rs6682737	ALX3	cis	parietal	SCAN
rs6682737	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs6682737	ST7L	cis	normal skin	skin_eQTL
rs6682737	ST7L	cis	lymphoblastoid	seeQTL
rs6682737	C1orf162	cis	parietal	SCAN
rs6682737	ST7L	cis	multi-tissue	Pritchard
rs6682737	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs6682737	ST7L	cis	lesional skin	skin_eQTL
rs6682737	ST7L	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
3	chr1:113109000-113160000	Weak transcription	Gastric	stomach
4	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
7	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
8	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
9	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:113119000-113138400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:113121000-113148400	Weak transcription	Stomach Mucosa	stomach
13	chr1:113124600-113148400	Weak transcription	NHLF	lung
14	chr1:113125000-113142000	Weak transcription	Hela-S3	cervix
15	chr1:113126800-113143400	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:113128000-113148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:113129000-113147200	Strong transcription	HSMM	muscle
18	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:113130200-113141000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:113131200-113137400	Strong transcription	Placenta	Placenta
21	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
22	chr1:113131600-113147200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:113132400-113136600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:113132600-113136800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:113132600-113139800	Weak transcription	NHEK	skin
26	chr1:113132600-113148400	Weak transcription	Lung	lung
27	chr1:113132600-113148400	Weak transcription	Pancreas	Pancrea
28	chr1:113132600-113148400	Weak transcription	Thymus	Thymus
29	chr1:113132600-113152400	Weak transcription	Psoas Muscle	Psoas
30	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:113132800-113139400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:113132800-113140000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:113132800-113143400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:113132800-113144200	Weak transcription	Right Ventricle	heart
36	chr1:113132800-113145400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:113133000-113136800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:113133000-113137000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:113133000-113137200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:113133000-113137600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:113133000-113137600	Weak transcription	Fetal Intestine Small	intestine
42	chr1:113133000-113137800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:113133000-113138000	Weak transcription	Left Ventricle	heart
44	chr1:113133000-113138200	Weak transcription	Fetal Stomach	stomach
45	chr1:113133000-113138800	Weak transcription	Primary T cells from cord blood	blood
46	chr1:113133000-113138800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:113133000-113139000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:113133000-113139400	Weak transcription	Brain Substantia Nigra	brain
49	chr1:113133000-113139600	Weak transcription	HMEC	breast
50	chr1:113133000-113142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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