Variant report

Variant	rs2164102
Chromosome Location	chr15:76857227-76857228
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	chr15:76855877..76857707-chr15:76866696..76869240,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1011083	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1011084	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10152247	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10851888	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10851889	0.81[EUR][1000 genomes]
rs11072597	0.81[AFR][1000 genomes]
rs11072598	0.81[AFR][1000 genomes]
rs11072600	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072602	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072607	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072610	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072612	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072616	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072618	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11629727	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11630402	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631394	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632670	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632765	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11635273	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11635463	0.81[AFR][1000 genomes]
rs11637096	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11852777	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11854850	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11855762	0.90[EUR][1000 genomes]
rs11857327	0.81[AFR][1000 genomes]
rs12437981	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440511	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12440965	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591622	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898810	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12904417	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12910081	0.81[EUR][1000 genomes]
rs12910820	0.81[EUR][1000 genomes]
rs12914196	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1603860	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809875	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2047504	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2120109	0.84[EUR][1000 genomes]
rs2404604	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404734	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2436996	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454450	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454451	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454454	0.83[ASN][1000 genomes]
rs2459361	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2461871	0.83[ASN][1000 genomes]
rs2469249	0.81[AFR][1000 genomes]
rs28895952	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34103231	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886805	0.81[AFR][1000 genomes]
rs4886816	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886819	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56339024	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57682236	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62026889	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62026898	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165053	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7181506	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029283	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs965818	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	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
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1038233	chr15:76855205-76895763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2164102	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2164102	SCAPER	cis	Artery Tibial	GTEx
rs2164102	SCAPER	cis	Whole Blood	GTEx
rs2164102	SCAPER	cis	Nerve Tibial	GTEx
rs2164102	SCAPER	cis	Muscle Skeletal	GTEx
rs2164102	SCAPER	cis	Esophagus Mucosa	GTEx
rs2164102	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2164102	SCAPER	cis	Esophagus Muscularis	GTEx
rs2164102	SCAPER	cis	lung	GTEx
rs2164102	SCAPER	cis	Thyroid	GTEx
rs2164102	SCAPER	cis	Adipose Subcutaneous	GTEx
rs2164102	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76846000-76862800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:76846000-76869000	Weak transcription	Left Ventricle	heart
3	chr15:76846000-76869000	Weak transcription	Pancreas	Pancrea
4	chr15:76846200-76868800	Weak transcription	Fetal Intestine Small	intestine
5	chr15:76847000-76868200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:76847200-76862400	Weak transcription	Dnd41	blood
7	chr15:76848200-76863000	Weak transcription	Primary T cells from cord blood	blood
8	chr15:76850200-76868400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:76851200-76862400	Weak transcription	Primary B cells from cord blood	blood
10	chr15:76852000-76867000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr15:76852800-76861800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:76856400-76863800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:76857000-76868800	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links