Variant report

Variant	rs1388585
Chromosome Location	chr12:40531691-40531692
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	chr12:40526853..40529105-chr12:40530805..40532717,2	MCF-7	breast:
2	12:40525880-40532672..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10506143	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs10506144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10506146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10506147	0.81[EUR][1000 genomes]
rs10506154	1.00[CEU][hapmap]
rs10878244	1.00[JPT][hapmap]
rs11174697	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11175186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11175593	0.81[EUR][1000 genomes]
rs11564107	0.81[EUR][1000 genomes]
rs11564108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11564117	1.00[ASN][1000 genomes]
rs11564123	1.00[JPT][hapmap]
rs11564131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11564152	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11564153	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11564185	1.00[CEU][hapmap]
rs11564187	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11564190	0.80[ASN][1000 genomes]
rs11564196	1.00[JPT][hapmap]
rs11564199	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11564209	1.00[CEU][hapmap]
rs11564210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11564212	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11564214	1.00[ASN][1000 genomes]
rs11564216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11564218	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs11564271	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12422544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422796	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12423419	1.00[JPT][hapmap]
rs12423551	1.00[JPT][hapmap]
rs12424040	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12424294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12425561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12426378	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12426643	1.00[ASN][1000 genomes]
rs12427022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12427245	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1388597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1463717	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17442924	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17443078	0.81[EUR][1000 genomes]
rs17443185	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17443206	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17443600	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17443656	1.00[CEU][hapmap]
rs17444054	1.00[JPT][hapmap]
rs17444103	1.00[CEU][hapmap]
rs17458549	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17458808	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461387	1.00[ASN][1000 genomes]
rs17461575	0.81[EUR][1000 genomes]
rs17465610	0.81[EUR][1000 genomes]
rs17466016	1.00[CEU][hapmap]
rs17483919	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17484003	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17484141	1.00[JPT][hapmap]
rs2131081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2244534	0.85[YRI][hapmap]
rs2244780	0.85[YRI][hapmap]
rs2253021	0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs2253171	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2253867	0.87[AFR][1000 genomes]
rs2638223	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2638235	0.85[YRI][hapmap]
rs2638241	0.85[YRI][hapmap]
rs2638243	0.85[YRI][hapmap]
rs2638261	1.00[YRI][hapmap]
rs2638265	1.00[YRI][hapmap]
rs2708403	0.83[YRI][hapmap]
rs2708405	0.82[YRI][hapmap]
rs2708406	0.85[YRI][hapmap]
rs2708416	0.85[YRI][hapmap]
rs2708460	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708461	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2708475	1.00[YRI][hapmap]
rs2708483	1.00[YRI][hapmap]
rs2708484	1.00[YRI][hapmap]
rs28365169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28365173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28365206	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs28365229	1.00[CEU][hapmap]
rs28365689	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28370649	1.00[CEU][hapmap]
rs28370650	1.00[CEU][hapmap]
rs28370664	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs28370682	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28370830	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4628750	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4767961	0.87[AMR][1000 genomes]
rs4767962	1.00[ASN][1000 genomes]
rs4767964	0.86[ASN][1000 genomes]
rs4767965	0.81[EUR][1000 genomes]
rs4768213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768226	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4768228	1.00[JPT][hapmap]
rs729215	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][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	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40530800-40532000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:40531200-40531800	Enhancers	NHDF-Ad	bronchial
3	chr12:40531200-40532000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:40531200-40532400	Enhancers	HMEC	breast
5	chr12:40531400-40532600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:40531400-40532600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:40531400-40532600	Enhancers	NHEK	skin
8	chr12:40531600-40532800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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