Variant report

Variant	rs7873152
Chromosome Location	chr9:15555458-15555459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10118359	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10119975	0.82[EUR][1000 genomes]
rs10120726	0.94[AFR][1000 genomes]
rs10121393	0.85[EUR][1000 genomes]
rs10121591	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10122339	0.83[EUR][1000 genomes]
rs10123042	0.85[EUR][1000 genomes]
rs1039813	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1039814	0.89[ASN][1000 genomes]
rs10481557	0.89[CEU][hapmap]
rs10733295	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs10738399	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10756671	0.81[CEU][hapmap]
rs10756673	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756674	0.89[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs10756676	0.84[ASN][1000 genomes]
rs10756677	0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs10756679	0.85[CEU][hapmap]
rs10756686	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs10756687	0.89[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs10756688	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs10756689	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs10756690	0.89[CEU][hapmap]
rs10756691	0.82[EUR][1000 genomes]
rs10756697	0.85[CEU][hapmap]
rs10810397	0.92[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10810399	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10810401	0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs10810402	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs10810407	0.81[ASN][1000 genomes]
rs10810408	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs10810416	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10810419	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10810422	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810424	0.86[EUR][1000 genomes]
rs10810426	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810427	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs10810428	0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs10810429	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10810430	0.83[EUR][1000 genomes]
rs10810438	0.96[CEU][hapmap]
rs10810439	0.89[CEU][hapmap]
rs10810440	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs10962066	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10962070	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs10962098	0.89[CEU][hapmap]
rs10962099	0.89[CEU][hapmap]
rs10962106	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10962110	0.85[CEU][hapmap]
rs10962121	0.83[EUR][1000 genomes]
rs10962123	0.83[EUR][1000 genomes]
rs10962125	0.83[EUR][1000 genomes]
rs10962126	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11792937	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11793900	0.82[EUR][1000 genomes]
rs12004358	0.83[EUR][1000 genomes]
rs12340969	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs12341679	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs12349323	0.82[EUR][1000 genomes]
rs12352779	0.82[EUR][1000 genomes]
rs12377371	0.96[CEU][hapmap]
rs13301516	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1355171	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1396706	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs1396707	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs1396708	0.85[CEU][hapmap]
rs1533040	0.89[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs1553728	0.85[CEU][hapmap]
rs169342	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1812686	0.84[ASN][1000 genomes]
rs183928	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1848582	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs192466	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2055772	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs2175080	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2175082	0.82[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs2382534	0.85[CEU][hapmap]
rs2457265	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2457637	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2663300	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs276432	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs276433	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs276435	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs276436	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs276441	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs276443	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs276444	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276447	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs276448	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs276449	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs276453	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs276454	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276455	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2821545	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs28410434	0.83[EUR][1000 genomes]
rs3119699	0.96[CEU][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3122702	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35057009	0.83[EUR][1000 genomes]
rs36086644	0.83[EUR][1000 genomes]
rs3955162	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432452	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs433849	0.96[CEU][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs442549	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs451878	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4740614	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740615	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs4740619	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs4740624	0.89[CEU][hapmap]
rs4741516	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4741519	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4741528	0.89[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4741534	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4741535	0.85[CEU][hapmap]
rs62573118	0.83[EUR][1000 genomes]
rs6474930	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6474931	0.88[CEU][hapmap]
rs6474944	0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs6474945	0.89[CEU][hapmap];0.84[JPT][hapmap]
rs6474946	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6474951	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6474952	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6474954	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs7023275	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7024640	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7025669	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs7030846	0.87[EUR][1000 genomes]
rs7031365	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7032755	0.82[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap]
rs7034484	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7034781	0.96[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs7035863	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7036172	0.89[CEU][hapmap]
rs7036285	0.83[EUR][1000 genomes]
rs7036674	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs7036875	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7037662	0.83[EUR][1000 genomes]
rs7037908	0.83[EUR][1000 genomes]
rs7042475	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7046351	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7389629	0.89[CEU][hapmap]
rs7467156	0.96[CEU][hapmap]
rs7467207	0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs770524	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7847144	0.85[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs7848511	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7851056	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7851323	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7859780	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs7860623	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7860869	0.96[CEU][hapmap]
rs7863088	0.89[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs7866629	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7874533	0.88[CEU][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs7875367	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9407624	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs954663	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs954664	0.82[EUR][1000 genomes]
rs9650684	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9696751	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv892630	chr9:15554960-15694690	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7873152	C9orf93	cis	parietal	SCAN
rs7873152	C9orf93	cis	brain	seeQTL
rs7873152	C9orf93	cis	cerebellum	SCAN
rs7873152	ADAMTSL1	cis	parietal	SCAN
rs7873152	INPP4B	trans	brain	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15553800-15576200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:15553800-15580600	Weak transcription	Ovary	ovary
3	chr9:15553800-15592600	Weak transcription	Left Ventricle	heart
4	chr9:15554000-15564400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:15554000-15590200	Weak transcription	Fetal Stomach	stomach
6	chr9:15554400-15579400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:15554600-15555600	Enhancers	Thymus	Thymus
8	chr9:15554600-15556400	Weak transcription	Fetal Brain Male	brain
9	chr9:15554600-15563600	Weak transcription	Fetal Thymus	thymus
10	chr9:15554600-15580800	Weak transcription	Brain Anterior Caudate	brain
11	chr9:15554800-15559400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:15554800-15559600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:15554800-15560800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:15555200-15559400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links