Variant report

Variant	rs7651407
Chromosome Location	chr3:48443816-48443817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48442729..48446947-chr3:48464942..48468489,4	MCF-7	breast:
2	chr3:48442075..48446343-chr3:48473380..48477493,6	MCF-7	breast:
3	chr3:48442321..48445623-chr3:48469193..48472197,3	MCF-7	breast:
4	chr3:48441736..48444624-chr3:48460288..48462791,2	MCF-7	breast:
5	chr3:48313829..48315747-chr3:48442766..48445683,2	MCF-7	breast:
6	chr3:48440673..48446097-chr3:48469254..48474939,10	MCF-7	breast:
7	chr3:48443208..48445959-chr3:48446995..48448568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164050	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1037773	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10470686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap]
rs1109227	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11130170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11130171	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs11797	0.92[ASW][hapmap];0.82[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs12491849	0.80[TSI][hapmap]
rs13069724	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs13076076	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs13314659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap]
rs1459242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap]
rs1563736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap]
rs2242150	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs2279077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2290822	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs2362450	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs2362452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2885510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3214041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap]
rs3774808	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs4858795	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs4858819	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6442117	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs6442118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap]
rs6442119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap]
rs6442120	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6776700	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6794875	1.00[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs725310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap]
rs730566	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs734071	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs7636044	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs898225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap]
rs922075	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs9311428	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs9812647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs9815103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs9838618	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs9849509	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs9876781	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs9883759	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs9883927	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7651407	CXCR6	cis	parietal	SCAN
rs7651407	NME6	cis	cerebellum	SCAN
rs7651407	ALAS1	cis	parietal	SCAN
rs7651407	AMT	cis	cerebellum	SCAN
rs7651407	AMT	cis	parietal	SCAN
rs7651407	ZNF589	cis	cerebellum	SCAN
rs7651407	C3orf18	cis	cerebellum	SCAN
rs7651407	SHISA5	cis	lymphoblastoid	seeQTL
rs7651407	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs7651407	ZNF589	cis	parietal	SCAN
rs7651407	SBK1	trans	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48435400-48449800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48439400-48445000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:48439400-48447800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:48440000-48444000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:48440200-48444800	Weak transcription	Fetal Lung	lung
6	chr3:48440400-48444200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:48440400-48444200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:48440600-48444400	Enhancers	Esophagus	oesophagus
9	chr3:48440800-48444000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:48440800-48444000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:48440800-48447800	Weak transcription	Fetal Kidney	kidney
12	chr3:48441000-48444200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:48441000-48444400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:48441200-48444200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:48441200-48444600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:48441400-48444400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:48441600-48444800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:48441600-48445200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:48441800-48445000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:48442000-48444800	Genic enhancers	HMEC	breast
21	chr3:48442000-48466200	Strong transcription	Fetal Intestine Small	intestine
22	chr3:48442000-48467400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:48442200-48464600	Strong transcription	Brain Germinal Matrix	brain
24	chr3:48442200-48466800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:48442400-48444000	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:48442400-48444000	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:48442400-48444600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:48442400-48444800	Genic enhancers	NHEK	skin
29	chr3:48442400-48445000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:48442400-48450200	Weak transcription	Stomach Mucosa	stomach
31	chr3:48442600-48444000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:48442600-48444200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:48442600-48444200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:48442600-48444400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:48442600-48444400	Enhancers	NHDF-Ad	bronchial
36	chr3:48442600-48444600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:48442600-48444800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:48442600-48444800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:48442600-48466600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:48442800-48444200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr3:48442800-48444400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:48442800-48444600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:48442800-48446400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:48443000-48444000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:48443000-48444000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:48443000-48444000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:48443000-48444200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:48443000-48444200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:48443000-48444200	Enhancers	Colon Smooth Muscle	Colon
50	chr3:48443000-48444200	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links