Variant report

Variant	rs7962107
Chromosome Location	chr12:56604489-56604490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56604431-56604558	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56510493..56513270-chr12:56604377..56607242,3	K562	blood:
2	chr12:56598742..56603625-chr12:56603929..56607820,7	K562	blood:

Variant related genes	Relation type
RNF41	TF binding region
ENSG00000181852	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10747763	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10876878	1.00[ASN][1000 genomes]
rs10876885	1.00[EUR][1000 genomes]
rs1091527	1.00[EUR][1000 genomes]
rs11171772	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11171777	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11171818	1.00[EUR][1000 genomes]
rs11171819	1.00[EUR][1000 genomes]
rs11171822	1.00[EUR][1000 genomes]
rs11575221	1.00[EUR][1000 genomes]
rs11575236	1.00[EUR][1000 genomes]
rs11830379	1.00[EUR][1000 genomes]
rs11832580	1.00[EUR][1000 genomes]
rs11833064	1.00[EUR][1000 genomes]
rs11834728	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11834873	1.00[EUR][1000 genomes]
rs11834948	1.00[EUR][1000 genomes]
rs11835018	1.00[EUR][1000 genomes]
rs11835310	1.00[EUR][1000 genomes]
rs12229022	0.95[ASN][1000 genomes]
rs12306512	1.00[EUR][1000 genomes]
rs12306670	1.00[ASW][hapmap];0.85[LWK][hapmap]
rs12318887	1.00[EUR][1000 genomes]
rs12320265	0.82[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12322356	1.00[EUR][1000 genomes]
rs1274502	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1274503	1.00[ASN][1000 genomes]
rs1405859	1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1626158	1.00[EUR][1000 genomes]
rs1689517	1.00[EUR][1000 genomes]
rs1689518	1.00[CHD][hapmap];1.00[EUR][1000 genomes]
rs1702872	1.00[EUR][1000 genomes]
rs17118333	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17118461	1.00[EUR][1000 genomes]
rs17118590	1.00[EUR][1000 genomes]
rs1918496	1.00[EUR][1000 genomes]
rs2035948	1.00[EUR][1000 genomes]
rs2271188	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2271190	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2271192	1.00[JPT][hapmap]
rs2277340	1.00[CHD][hapmap]
rs2463365	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2629445	1.00[EUR][1000 genomes]
rs2629451	1.00[ASN][1000 genomes]
rs2629453	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2640566	1.00[EUR][1000 genomes]
rs2661728	1.00[EUR][1000 genomes]
rs2661729	1.00[EUR][1000 genomes]
rs2695783	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2695784	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2855320	1.00[MEX][hapmap]
rs28676339	0.83[ASN][1000 genomes]
rs2930788	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2934152	1.00[EUR][1000 genomes]
rs2950573	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34102859	1.00[MEX][hapmap]
rs3759096	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3802996	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809130	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4301822	1.00[EUR][1000 genomes]
rs4417324	1.00[EUR][1000 genomes]
rs4759218	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55887836	0.84[AFR][1000 genomes]
rs56163805	0.83[AFR][1000 genomes]
rs56696262	1.00[EUR][1000 genomes]
rs56851901	0.83[ASN][1000 genomes]
rs57237559	1.00[EUR][1000 genomes]
rs57280585	0.83[ASN][1000 genomes]
rs57387549	1.00[EUR][1000 genomes]
rs57822276	0.83[ASN][1000 genomes]
rs57990974	1.00[EUR][1000 genomes]
rs58009483	1.00[ASN][1000 genomes]
rs58349500	1.00[EUR][1000 genomes]
rs58476735	0.83[ASN][1000 genomes]
rs58548156	0.83[ASN][1000 genomes]
rs58663297	0.83[ASN][1000 genomes]
rs59053322	1.00[ASN][1000 genomes]
rs59078852	1.00[ASN][1000 genomes]
rs59286728	1.00[EUR][1000 genomes]
rs59794023	1.00[EUR][1000 genomes]
rs59966703	1.00[ASN][1000 genomes]
rs60011575	0.81[AFR][1000 genomes]
rs60396934	0.83[ASN][1000 genomes]
rs61733171	1.00[EUR][1000 genomes]
rs61733875	1.00[EUR][1000 genomes]
rs61939011	1.00[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6581093	1.00[EUR][1000 genomes]
rs703823	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7136420	1.00[ASW][hapmap];0.85[LWK][hapmap]
rs72478990	1.00[EUR][1000 genomes]
rs7298109	1.00[EUR][1000 genomes]
rs7300292	1.00[EUR][1000 genomes]
rs7304690	1.00[EUR][1000 genomes]
rs7309327	1.00[EUR][1000 genomes]
rs7310292	1.00[EUR][1000 genomes]
rs7311008	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73324353	1.00[EUR][1000 genomes]
rs73324358	1.00[EUR][1000 genomes]
rs73338377	1.00[EUR][1000 genomes]
rs73338385	1.00[EUR][1000 genomes]
rs74094726	1.00[EUR][1000 genomes]
rs7489249	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs773654	1.00[ASN][1000 genomes]
rs773655	0.90[ASN][1000 genomes]
rs773658	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs773659	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs773660	0.90[ASN][1000 genomes]
rs773661	1.00[ASN][1000 genomes]
rs7954155	1.00[EUR][1000 genomes]
rs7954200	1.00[EUR][1000 genomes]
rs7956599	0.81[ASN][1000 genomes]
rs7956926	0.81[ASN][1000 genomes]
rs7957187	1.00[EUR][1000 genomes]
rs7958958	1.00[EUR][1000 genomes]
rs7967464	1.00[ASN][1000 genomes]
rs7975405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977692	1.00[EUR][1000 genomes]
rs7979812	1.00[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56585000-56614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56592600-56613600	Weak transcription	Right Atrium	heart
3	chr12:56597800-56610600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:56597800-56610600	Strong transcription	Fetal Lung	lung
5	chr12:56597800-56611600	Strong transcription	Primary T cells from cord blood	blood
6	chr12:56597800-56611600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:56597800-56611800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:56597800-56611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:56597800-56611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:56597800-56611800	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:56597800-56611800	Strong transcription	Fetal Thymus	thymus
12	chr12:56597800-56612000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:56598000-56606400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr12:56598000-56610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:56598000-56610600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:56598000-56610600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:56598000-56610600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:56598000-56610600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:56598000-56610600	Strong transcription	Brain Hippocampus Middle	brain
20	chr12:56598000-56610600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr12:56598000-56610600	Strong transcription	Spleen	Spleen
22	chr12:56598000-56611000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:56598000-56611000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr12:56598000-56611600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:56598000-56611600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:56598000-56611600	Strong transcription	Fetal Brain Female	brain
27	chr12:56598000-56611600	Strong transcription	Fetal Intestine Large	intestine
28	chr12:56598000-56611600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:56598000-56611800	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr12:56598000-56613600	Strong transcription	Fetal Stomach	stomach
31	chr12:56598200-56609000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:56598200-56609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:56598200-56610400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:56598200-56610600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr12:56598200-56610600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:56598200-56610600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:56598200-56610600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:56598200-56610600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:56598200-56611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:56598200-56611800	Strong transcription	Placenta	Placenta
41	chr12:56598200-56611800	Strong transcription	Thymus	Thymus
42	chr12:56598200-56613800	Strong transcription	Fetal Intestine Small	intestine
43	chr12:56598400-56610600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:56598400-56610600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:56598400-56610600	Strong transcription	HSMMtube	muscle
46	chr12:56598400-56610800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:56598400-56611400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:56598400-56611800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:56598400-56611800	Strong transcription	Brain Germinal Matrix	brain
50	chr12:56598600-56606200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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