Variant report

Variant	rs157783
Chromosome Location	chr15:76765239-76765240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10851888	0.83[CHB][hapmap]
rs11072591	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072597	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11072598	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11072610	0.83[CHB][hapmap]
rs11072612	0.82[CHB][hapmap]
rs11629888	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11632222	0.83[ASN][1000 genomes]
rs11634019	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11635463	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11637096	0.86[CHB][hapmap]
rs11637490	0.92[ASN][1000 genomes]
rs11638767	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11856717	0.83[CHB][hapmap]
rs11857015	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11857327	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12437627	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs12437981	0.83[CHB][hapmap]
rs12440965	0.83[CHB][hapmap]
rs12591100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.89[ASN][1000 genomes]
rs12900179	0.84[ASN][1000 genomes]
rs12904417	0.83[CHB][hapmap]
rs12906143	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12907805	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs12909656	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12914005	0.82[AMR][1000 genomes]
rs12915248	0.95[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs1587381	0.95[MEX][hapmap];0.84[TSI][hapmap]
rs1607015	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1607017	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17362383	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs17364076	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs17364330	0.95[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs17460201	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs2047504	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2048856	0.88[ASN][1000 genomes]
rs206205	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280306	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2404734	0.83[CHB][hapmap]
rs2436994	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2454450	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2454451	0.83[CHB][hapmap]
rs2454454	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2459361	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2461870	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2461871	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2461872	0.85[CHB][hapmap]
rs2468130	0.86[ASN][1000 genomes]
rs2468131	0.88[ASN][1000 genomes]
rs2469249	0.95[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs283789	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs283793	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs283795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284891	0.93[ASN][1000 genomes]
rs284892	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284895	0.81[MEX][hapmap];0.82[TSI][hapmap]
rs284899	0.87[ASN][1000 genomes]
rs284909	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2944378	0.93[ASN][1000 genomes]
rs2957614	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3765115	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3866543	0.81[MEX][hapmap]
rs437131	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886488	0.82[JPT][hapmap]
rs4886489	0.82[CHB][hapmap]
rs4886493	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886495	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886794	0.83[CHB][hapmap]
rs4886798	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886800	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886805	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886816	0.82[CHB][hapmap]
rs4886819	0.83[CHB][hapmap]
rs62028406	0.84[ASN][1000 genomes]
rs62028423	0.91[ASN][1000 genomes]
rs62028434	0.92[ASN][1000 genomes]
rs7163946	0.81[AMR][1000 genomes]
rs7164813	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7165025	0.82[AMR][1000 genomes]
rs7181506	0.83[CHB][hapmap]
rs744336	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[ASN][1000 genomes]
rs8029283	0.81[CHB][hapmap]
rs8030411	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs8037847	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs908817	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs965818	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv974602	chr15:76764286-76765752	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs157783	SCAPER	cis	Whole Blood	GTEx
rs157783	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs157783	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs157783	SCAPER	cis	Nerve Tibial	GTEx
rs157783	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs157783	RP11-685G9.2	cis	Whole Blood	GTEx
rs157783	ISL2	cis	Whole Blood	GTEx
rs157783	SCAPER	cis	Esophagus Muscularis	GTEx
rs157783	ZNF291	cis	multi-tissue	Pritchard
rs157783	SCAPER	cis	lung	GTEx
rs157783	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76711600-76767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
3	chr15:76758400-76765600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr15:76759800-76770400	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:76760000-76772600	Weak transcription	GM12878-XiMat	blood
6	chr15:76760400-76773800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:76761400-76765400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:76762000-76771400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:76762800-76765400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:76762800-76765600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:76762800-76771200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:76763000-76768200	Weak transcription	Ovary	ovary
13	chr15:76763000-76768600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:76763000-76795000	Weak transcription	Primary B cells from cord blood	blood
15	chr15:76763200-76770200	Weak transcription	Adipose Nuclei	Adipose
16	chr15:76763400-76767200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:76763600-76765800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:76763600-76775200	Weak transcription	Liver	Liver
19	chr15:76764200-76766000	Weak transcription	Primary T cells from cord blood	blood
20	chr15:76764200-76766000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:76764200-76767000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links