Variant report

Variant	rs7873746
Chromosome Location	chr9:102775717-102775718
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102579598..102582275-chr9:102774646..102777784,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237461	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10739795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10739796	0.96[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs10760710	0.85[EUR][1000 genomes]
rs10760712	0.86[EUR][1000 genomes]
rs10819716	0.85[EUR][1000 genomes]
rs10819717	0.86[EUR][1000 genomes]
rs10819719	0.84[EUR][1000 genomes]
rs10819737	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs10988945	0.85[JPT][hapmap]
rs10988973	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs11555502	0.81[EUR][1000 genomes]
rs12336751	0.85[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs12552646	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs1342147	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs1406613	0.85[EUR][1000 genomes]
rs1418267	0.81[EUR][1000 genomes]
rs1529191	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs1529192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1534726	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1535667	0.85[JPT][hapmap]
rs1578644	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1578645	0.86[EUR][1000 genomes]
rs1852864	0.85[EUR][1000 genomes]
rs1852865	0.85[EUR][1000 genomes]
rs1999877	1.00[CHD][hapmap]
rs2057476	0.85[JPT][hapmap]
rs2104273	0.86[EUR][1000 genomes]
rs2181579	1.00[CHD][hapmap]
rs2476441	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs2698999	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs2761056	0.96[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs2787361	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs2787366	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs2795575	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs2806682	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs4428721	0.81[ASW][hapmap]
rs4495492	0.83[EUR][1000 genomes]
rs4503155	0.85[EUR][1000 genomes]
rs4517187	1.00[CHD][hapmap]
rs4742779	0.85[JPT][hapmap]
rs4743375	0.86[EUR][1000 genomes]
rs4743376	0.86[EUR][1000 genomes]
rs6478991	0.85[EUR][1000 genomes]
rs6478994	0.86[EUR][1000 genomes]
rs6478995	0.81[EUR][1000 genomes]
rs6478996	0.86[EUR][1000 genomes]
rs6478997	0.86[EUR][1000 genomes]
rs6478998	0.86[EUR][1000 genomes]
rs6479000	0.83[EUR][1000 genomes]
rs6479001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs6479002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7024016	0.83[EUR][1000 genomes]
rs7026532	0.86[EUR][1000 genomes]
rs7027414	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs7029020	0.85[EUR][1000 genomes]
rs7029048	0.85[EUR][1000 genomes]
rs7032333	0.84[EUR][1000 genomes]
rs7033091	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs7037362	0.81[EUR][1000 genomes]
rs7041338	0.83[EUR][1000 genomes]
rs7042912	0.86[EUR][1000 genomes]
rs7043057	0.83[EUR][1000 genomes]
rs7846794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7847213	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7853485	0.85[EUR][1000 genomes]
rs7857530	0.85[EUR][1000 genomes]
rs7861003	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap]
rs7865257	0.81[ASW][hapmap]
rs846752	0.85[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs846753	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs846756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs846759	0.85[JPT][hapmap]
rs846761	0.96[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs846766	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs846770	0.96[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs860171	0.96[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs9886877	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.86[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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7873746	INVS	cis	cerebellum	SCAN
rs7873746	MURC	cis	parietal	SCAN
rs7873746	TBC1D22B	cis	Cerebellum	GTEx
rs7873746	STX17	cis	Stomach	GTEx
rs7873746	STX17	cis	Esophagus Mucosa	GTEx
rs7873746	INVS	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102718000-102777600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:102729600-102826800	Weak transcription	HMEC	breast
3	chr9:102731000-102778200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:102757400-102790600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:102759600-102777000	Weak transcription	HUVEC	blood vessel
6	chr9:102760800-102783400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:102761000-102778200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:102762000-102790000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:102763400-102783400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:102764200-102783200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:102765200-102777000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:102766200-102778200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr9:102766400-102783400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:102766400-102784600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:102766400-102785400	Weak transcription	Fetal Brain Male	brain
16	chr9:102766400-102787000	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:102766400-102794800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:102766600-102787200	Weak transcription	Psoas Muscle	Psoas
19	chr9:102766800-102783400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:102766800-102784600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr9:102766800-102793000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:102767000-102778000	Weak transcription	Fetal Stomach	stomach
23	chr9:102767000-102778200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:102767000-102781400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:102767000-102783400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:102767000-102783400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:102767000-102783400	Weak transcription	NHEK	skin
28	chr9:102767000-102785200	Weak transcription	Brain Substantia Nigra	brain
29	chr9:102767000-102785400	Weak transcription	Brain Germinal Matrix	brain
30	chr9:102767000-102787800	Weak transcription	Right Ventricle	heart
31	chr9:102767000-102799400	Weak transcription	Spleen	Spleen
32	chr9:102767000-102820400	Weak transcription	Colonic Mucosa	Colon
33	chr9:102767200-102776800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:102767200-102777000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:102767200-102784800	Weak transcription	A549	lung
36	chr9:102767200-102789800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr9:102767200-102821800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr9:102767600-102776400	Weak transcription	Thymus	Thymus
39	chr9:102767600-102776600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:102767600-102776600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:102767600-102776800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:102767600-102776800	Weak transcription	Fetal Thymus	thymus
43	chr9:102767600-102777000	Weak transcription	Fetal Lung	lung
44	chr9:102767600-102777000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:102767600-102778000	Weak transcription	Aorta	Aorta
46	chr9:102767600-102778000	Weak transcription	Esophagus	oesophagus
47	chr9:102767600-102781800	Weak transcription	HepG2	liver
48	chr9:102767600-102783400	Weak transcription	Lung	lung
49	chr9:102767600-102785800	Weak transcription	Pancreas	Pancrea
50	chr9:102767600-102788200	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links