Variant report

Variant	rs6509628
Chromosome Location	chr19:52741712-52741713
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52732749..52736646-chr19:52736909..52741775,7	K562	blood:
2	chr19:52692341..52695261-chr19:52740716..52742610,2	MCF-7	breast:
3	chr19:52707646..52710337-chr19:52740110..52742773,2	K562	blood:
4	chr19:52741136..52742682-chr19:52743584..52745481,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105568	Chromatin interaction
ENSG00000268015	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10402209	0.96[ASN][1000 genomes]
rs10402638	0.96[ASN][1000 genomes]
rs10403154	0.81[CHD][hapmap]
rs10403283	0.98[ASN][1000 genomes]
rs10403311	0.87[ASN][1000 genomes]
rs10403806	0.96[ASN][1000 genomes]
rs10404437	0.96[ASN][1000 genomes]
rs10407063	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10407502	1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10408119	1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10411211	0.98[ASN][1000 genomes]
rs10412110	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10412196	0.92[ASN][1000 genomes]
rs10413012	0.98[ASN][1000 genomes]
rs10413435	0.83[CHD][hapmap]
rs10414083	1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10414197	1.00[CHB][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs10414423	1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10414536	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10414852	0.96[ASN][1000 genomes]
rs10416785	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10417033	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10417253	1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10417820	0.95[CHD][hapmap]
rs10418666	0.83[ASN][1000 genomes]
rs10419304	0.95[CHD][hapmap]
rs10420207	0.85[ASN][1000 genomes]
rs10420560	0.96[ASN][1000 genomes]
rs10421589	0.87[ASN][1000 genomes]
rs10422838	1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10423125	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10424348	0.89[MEX][hapmap]
rs10425135	1.00[CHD][hapmap];0.96[ASN][1000 genomes]
rs10426002	0.98[ASN][1000 genomes]
rs10426786	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1056348	0.81[CHD][hapmap]
rs13344984	0.89[MEX][hapmap]
rs16983549	0.89[MEX][hapmap]
rs16983598	0.95[CHD][hapmap];0.96[ASN][1000 genomes]
rs16983601	0.96[ASN][1000 genomes]
rs16983603	1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[ASN][1000 genomes]
rs16983610	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16983619	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs16983648	0.83[AFR][1000 genomes]
rs17835942	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2115074	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2288409	0.95[CHD][hapmap]
rs2303685	0.95[CHD][hapmap]
rs2560871	1.00[JPT][hapmap]
rs2560873	1.00[JPT][hapmap]
rs28444225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28563055	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745097	0.94[CHD][hapmap]
rs4327163	0.86[AFR][1000 genomes]
rs55751302	0.98[ASN][1000 genomes]
rs55871532	0.98[ASN][1000 genomes]
rs57102373	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs57370252	0.86[AFR][1000 genomes]
rs60063830	0.98[ASN][1000 genomes]
rs60307688	0.86[AFR][1000 genomes]
rs6509629	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs7249460	0.81[CHD][hapmap];0.98[ASN][1000 genomes]
rs7250109	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs7255058	0.94[ASN][1000 genomes]
rs7255677	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7255737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7256300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259175	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs73935052	0.96[ASN][1000 genomes]
rs73935053	0.98[ASN][1000 genomes]
rs73935058	0.86[AFR][1000 genomes]
rs755531	0.95[CHD][hapmap]
rs8100048	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs8100500	0.95[CHD][hapmap]
rs8100600	0.89[CHD][hapmap]
rs8101990	0.83[CHD][hapmap]
rs8105432	0.96[ASN][1000 genomes]
rs8106271	0.81[CHD][hapmap]
rs8106544	0.90[ASN][1000 genomes]
rs8108636	0.96[ASN][1000 genomes]
rs8109061	0.80[ASN][1000 genomes]
rs8109512	0.96[ASN][1000 genomes]
rs8110857	0.96[ASN][1000 genomes]
rs8110881	0.96[ASN][1000 genomes]
rs8113537	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52733200-52742800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:52733200-52759600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:52734400-52751600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr19:52734600-52743800	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links