Variant report

Variant	rs2638223
Chromosome Location	chr12:40536581-40536582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-1	chr12:40534728-40536678	ENSG00000260943.1

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10506143	1.00[JPT][hapmap]
rs10506144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs10506146	1.00[JPT][hapmap]
rs10506147	0.86[EUR][1000 genomes]
rs10506154	1.00[CEU][hapmap]
rs10878244	1.00[JPT][hapmap]
rs11174697	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11175186	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11175593	0.86[EUR][1000 genomes]
rs11564107	0.86[EUR][1000 genomes]
rs11564108	1.00[JPT][hapmap]
rs11564117	0.93[ASN][1000 genomes]
rs11564123	1.00[JPT][hapmap]
rs11564131	1.00[JPT][hapmap]
rs11564152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11564153	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11564185	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11564187	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11564196	1.00[JPT][hapmap]
rs11564199	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11564209	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11564210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11564212	0.86[EUR][1000 genomes]
rs11564214	0.93[ASN][1000 genomes]
rs11564216	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11564218	1.00[JPT][hapmap]
rs11564271	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12422544	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12422796	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12423419	1.00[JPT][hapmap]
rs12423551	1.00[JPT][hapmap]
rs12424040	0.93[EUR][1000 genomes]
rs12424294	1.00[JPT][hapmap]
rs12425561	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12426378	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12426643	0.93[ASN][1000 genomes]
rs12427022	1.00[JPT][hapmap]
rs12427245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1388585	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1388597	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1463717	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17442924	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17443078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17443178	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17443185	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17443206	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17443600	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17443656	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17443909	0.86[EUR][1000 genomes]
rs17444028	0.81[EUR][1000 genomes]
rs17444054	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17444103	1.00[CEU][hapmap]
rs17458549	0.93[EUR][1000 genomes]
rs17458808	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17461387	0.93[ASN][1000 genomes]
rs17461575	0.86[EUR][1000 genomes]
rs17461664	0.81[EUR][1000 genomes]
rs17465610	0.86[EUR][1000 genomes]
rs17465946	0.86[EUR][1000 genomes]
rs17466016	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17483919	0.93[ASN][1000 genomes]
rs17484003	0.93[EUR][1000 genomes]
rs17484141	1.00[JPT][hapmap]
rs17484342	0.81[EUR][1000 genomes]
rs2131081	1.00[JPT][hapmap]
rs2244534	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2244780	0.85[YRI][hapmap]
rs2253021	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs2253171	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2253867	1.00[AFR][1000 genomes]
rs2638235	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2638236	0.86[AFR][1000 genomes]
rs2638237	0.86[AFR][1000 genomes]
rs2638240	0.86[AFR][1000 genomes]
rs2638241	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2638243	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2638261	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2638265	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2708403	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs2708405	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs2708406	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2708410	0.86[AFR][1000 genomes]
rs2708415	0.86[AFR][1000 genomes]
rs2708416	0.85[YRI][hapmap]
rs2708460	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708461	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2708462	0.86[AFR][1000 genomes]
rs2708471	0.86[AFR][1000 genomes]
rs2708475	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2708483	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2708484	1.00[YRI][hapmap]
rs28365169	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs28365173	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs28365229	1.00[CEU][hapmap]
rs28365689	0.93[EUR][1000 genomes]
rs28370649	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs28370650	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs28370664	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs28370682	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs28370830	0.86[EUR][1000 genomes]
rs36212067	0.81[EUR][1000 genomes]
rs36220738	0.81[EUR][1000 genomes]
rs4628750	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4767962	0.93[ASN][1000 genomes]
rs4767965	0.86[EUR][1000 genomes]
rs4768213	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4768226	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4768228	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs72547977	0.86[EUR][1000 genomes]
rs729215	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv519063	chr12:40536061-40538858	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40532800-40543800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40535000-40537200	Enhancers	Hela-S3	cervix
3	chr12:40535600-40536600	Enhancers	HMEC	breast
4	chr12:40535600-40536600	Enhancers	NHEK	skin
5	chr12:40536000-40536600	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links