Variant report

Variant	rs7960478
Chromosome Location	chr12:44402928-44402929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TWF1-1	chr12:44402423-44403946	NONHSAT027810

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10880617	1.00[JPT][hapmap]
rs11182385	0.83[AMR][1000 genomes]
rs12230287	0.83[AMR][1000 genomes]
rs12311962	1.00[JPT][hapmap]
rs12314126	1.00[JPT][hapmap]
rs13377809	1.00[JPT][hapmap]
rs1532218	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675765	1.00[JPT][hapmap]
rs1675771	1.00[JPT][hapmap]
rs1675778	1.00[JPT][hapmap]
rs1675782	1.00[JPT][hapmap]
rs1675788	1.00[JPT][hapmap]
rs1675791	1.00[JPT][hapmap]
rs17093973	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17093993	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17094007	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121301	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1731439	1.00[JPT][hapmap]
rs1731440	1.00[JPT][hapmap]
rs1731442	1.00[JPT][hapmap]
rs2407791	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3929354	0.83[AMR][1000 genomes]
rs55641600	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55657021	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55773976	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55913788	1.00[ASN][1000 genomes]
rs55917469	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56008731	1.00[ASN][1000 genomes]
rs56011342	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56081380	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56114967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56122564	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56168228	1.00[ASN][1000 genomes]
rs56227915	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56322120	1.00[ASN][1000 genomes]
rs56337317	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56355753	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57066844	1.00[ASN][1000 genomes]
rs57331385	1.00[ASN][1000 genomes]
rs58938395	1.00[ASN][1000 genomes]
rs60120002	1.00[ASN][1000 genomes]
rs61930676	1.00[ASN][1000 genomes]
rs61930689	1.00[ASN][1000 genomes]
rs61930691	1.00[ASN][1000 genomes]
rs61930693	1.00[ASN][1000 genomes]
rs7132451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136217	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71435964	1.00[ASN][1000 genomes]
rs7303909	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73085758	0.98[EUR][1000 genomes]
rs73085764	1.00[EUR][1000 genomes]
rs73085767	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73085788	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087603	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087605	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087610	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087626	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087664	0.98[EUR][1000 genomes]
rs73087684	0.83[AMR][1000 genomes]
rs73087687	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087696	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087700	0.83[AMR][1000 genomes]
rs73087702	0.98[EUR][1000 genomes]
rs73089730	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089734	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089739	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73089744	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089748	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089753	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089761	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73091736	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091741	0.98[EUR][1000 genomes]
rs73091745	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7311778	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959226	0.83[AMR][1000 genomes]
rs7971036	1.00[ASN][1000 genomes]
rs7980005	0.83[AMR][1000 genomes]
rs9783422	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9783507	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919711	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919742	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832390	chr12:44318071-44512114	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1041188	chr12:44331098-44528712	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832391	chr12:44394137-44552555	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44390800-44439200	Weak transcription	Esophagus	oesophagus
2	chr12:44394600-44403200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:44401400-44403600	ZNF genes & repeats	Fetal Intestine Large	intestine
4	chr12:44401400-44403800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:44401400-44404000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:44401600-44403400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr12:44401800-44403000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr12:44401800-44403200	ZNF genes & repeats	HMEC	breast
9	chr12:44402000-44432200	Weak transcription	Aorta	Aorta
10	chr12:44402400-44403000	ZNF genes & repeats	HSMM	muscle
11	chr12:44402600-44403600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:44402800-44403800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:44402800-44414600	Weak transcription	HSMMtube	muscle

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