Variant report

Variant	rs9902643
Chromosome Location	chr17:67191448-67191449
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1011789	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs1024598	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs10775358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10775359	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077403	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs1158495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652530	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs11656539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12453914	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12601388	0.85[ASN][1000 genomes]
rs12939282	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12940298	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12952117	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12953127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558166	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1968100	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1974577	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2041170	0.85[ASN][1000 genomes]
rs2041171	0.86[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2108738	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2190900	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2215148	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364986	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364991	0.83[GIH][hapmap]
rs2364992	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs2364993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3744489	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4141177	1.00[ASW][hapmap];0.81[CHD][hapmap]
rs4334355	0.84[ASN][1000 genomes]
rs4577157	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4603621	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs4968785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968838	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs4968839	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs4968843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6501183	0.84[ASN][1000 genomes]
rs7208586	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs7210259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213831	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs7216899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7217887	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740518	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs740520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8064583	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs8064595	0.86[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs8066449	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8071373	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs8071611	0.82[GIH][hapmap]
rs8074654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077252	1.00[ASW][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap]
rs8077551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8078314	0.84[ASN][1000 genomes]
rs8079981	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs8080693	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs8080863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8081003	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303012	0.83[ASN][1000 genomes]
rs976698	0.83[ASN][1000 genomes]
rs981452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981453	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs9891283	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9892172	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894689	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9898868	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899837	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902996	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9904672	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909083	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9909216	0.87[GIH][hapmap]
rs9911770	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9912127	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9916084	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9916693	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs997781	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv575930	chr17:67120025-67212031	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457888	chr17:67149973-67226643	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv575931	chr17:67149973-67226643	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv575933	chr17:67153386-67215712	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9902643	CACNG5	cis	cerebellum	SCAN
rs9902643	TEX2	cis	parietal	SCAN
rs9902643	MRC2	cis	parietal	SCAN
rs9902643	ABCA6	cis	cerebellum	SCAN
rs9902643	ABCA6	cis	parietal	SCAN
rs9902643	ABCA8	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
2	chr17:67150800-67192400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr17:67150800-67193200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr17:67160600-67220000	Weak transcription	Fetal Lung	lung
5	chr17:67173200-67193000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr17:67173400-67230000	Weak transcription	Pancreas	Pancrea
7	chr17:67176600-67193400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:67177800-67192000	Weak transcription	Fetal Intestine Large	intestine
9	chr17:67180600-67209000	Weak transcription	Ovary	ovary
10	chr17:67184600-67192200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:67189600-67208600	Weak transcription	Liver	Liver
12	chr17:67189600-67209000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr17:67189800-67195800	Weak transcription	Adipose Nuclei	Adipose
14	chr17:67189800-67221400	Weak transcription	Right Ventricle	heart
15	chr17:67190600-67193400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links