Variant report

Variant	rs17765653
Chromosome Location	chr6:12319527-12319528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10947946	0.83[CHB][hapmap]
rs10947948	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947949	0.80[AMR][1000 genomes]
rs11752276	0.80[ASN][1000 genomes]
rs11753558	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11757019	0.90[ASN][1000 genomes]
rs12055484	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2032549	0.86[ASN][1000 genomes]
rs4379286	0.84[CHD][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711654	0.91[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4711655	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4714383	0.80[JPT][hapmap]
rs4714384	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4714418	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56058129	0.83[AFR][1000 genomes]
rs6458193	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6921790	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6932390	0.84[EUR][1000 genomes]
rs9357344	0.83[CHB][hapmap]
rs9357346	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9369262	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9381015	0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9381033	0.83[ASW][hapmap];0.82[CEU][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9381035	0.91[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394741	0.87[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	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17765653	EDN1	Cis_1M	lymphoblastoid	RTeQTL
rs17765653	GMPR	cis	cerebellum	SCAN
rs17765653	RN7SKP293	cis	Artery Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12315200-12327800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:12317600-12320000	ZNF genes & repeats	A549	lung
3	chr6:12318800-12319600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:12319000-12319800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:12319000-12320000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:12319200-12324600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:12319400-12320200	Enhancers	GM12878-XiMat	blood
8	chr6:12319400-12324200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:12319400-12324400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:12319400-12324400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:12319400-12325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links