Variant report

Variant	rs6804650
Chromosome Location	chr3:160648953-160648954
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	chr3:160473266..160475652-chr3:160647072..160650166,3	MCF-7	breast:
2	chr3:160643537..160645831-chr3:160647633..160653129,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1037888	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10513559	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[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513562	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11708076	0.85[ASN][1000 genomes]
rs11708813	1.00[CEU][hapmap]
rs11716265	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11922752	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12639128	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13064176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071909	0.82[EUR][1000 genomes]
rs13073571	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086250	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13089559	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]
rs13092102	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13097130	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1374793	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1447618	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1447619	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1447620	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1610158	0.89[CEU][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs17236725	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17236746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17826438	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839021	0.84[EUR][1000 genomes]
rs2121718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2306061	0.85[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs2593812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs34168351	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34297047	0.85[EUR][1000 genomes]
rs4342141	0.81[CEU][hapmap]
rs4557202	0.85[CEU][hapmap]
rs4679662	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4679666	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4679671	0.82[EUR][1000 genomes]
rs4679922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679924	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs5004752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs55672403	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55888276	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61105146	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270274	0.81[EUR][1000 genomes]
rs62270275	0.81[EUR][1000 genomes]
rs62280303	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280331	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62280333	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441339	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6441354	0.85[CEU][hapmap]
rs6764019	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6796201	0.85[EUR][1000 genomes]
rs6799160	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6806054	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6809177	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[EUR][1000 genomes]
rs723757	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622047	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7628880	0.81[EUR][1000 genomes]
rs7632423	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs778642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs778643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs778645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs778646	0.86[EUR][1000 genomes]
rs778649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs778653	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs778654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs778657	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs778663	0.83[EUR][1000 genomes]
rs796609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs898680	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs898681	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs9290065	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs9790132	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs980975	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs980976	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9811594	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs9820825	0.87[CEU][hapmap]
rs9831488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9847866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9860360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9875200	1.00[CEU][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6804650	PPM1L	cis	cerebellum	SCAN
rs6804650	NMD3	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160635400-160649200	Weak transcription	Fetal Brain Female	brain
2	chr3:160644800-160654400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:160647200-160650200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:160647600-160649000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:160647600-160649000	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:160647600-160650400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:160647600-160652400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:160647800-160649000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:160647800-160649200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:160647800-160649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:160648000-160649000	Weak transcription	NHLF	lung
12	chr3:160648000-160649200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:160648000-160653200	Weak transcription	Adipose Nuclei	Adipose
14	chr3:160648400-160649200	Enhancers	Fetal Brain Male	brain
15	chr3:160648400-160650200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:160648400-160650400	Enhancers	NHDF-Ad	bronchial
17	chr3:160648600-160649400	Enhancers	Fetal Heart	heart
18	chr3:160648800-160650600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links