Variant report

Variant	rs12692962
Chromosome Location	chr2:172003251-172003252
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172002500..172008778-chr2:172012564..172018500,9	MCF-7	breast:
2	chr2:172001492..172003805-chr2:172016771..172018907,2	MCF-7	breast:
3	chr2:171829864..171832222-chr2:172003176..172005661,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10177560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10182205	0.97[ASN][1000 genomes]
rs10182207	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183486	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10189480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10191270	1.00[CHB][hapmap]
rs10193992	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10197081	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10198197	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10199500	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs10206289	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10207361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10208271	0.81[ASN][1000 genomes]
rs10208341	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10210693	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10210791	0.81[ASN][1000 genomes]
rs10210883	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1025240	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1025241	0.81[ASN][1000 genomes]
rs1025242	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035825	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1035826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1035828	1.00[CHB][hapmap]
rs1045327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10930453	1.00[CHB][hapmap]
rs10930455	1.00[CHB][hapmap]
rs10930456	1.00[CHB][hapmap]
rs10930457	1.00[CHB][hapmap]
rs11553951	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12612871	1.00[CHB][hapmap]
rs12997252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs12998296	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs13000644	0.85[EUR][1000 genomes]
rs13000898	0.85[EUR][1000 genomes]
rs13001088	0.85[EUR][1000 genomes]
rs13002517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13003218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13004273	1.00[CHB][hapmap]
rs13006705	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13007415	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13008199	1.00[CHB][hapmap]
rs13010307	1.00[CHB][hapmap]
rs13016705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13026444	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13028857	0.83[EUR][1000 genomes]
rs13030784	1.00[CHB][hapmap]
rs13034529	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13036123	1.00[CHB][hapmap]
rs13395669	0.81[ASN][1000 genomes]
rs13401706	0.81[ASN][1000 genomes]
rs13402107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13403285	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13411575	1.00[CHB][hapmap]
rs13417709	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13417864	0.90[ASN][1000 genomes]
rs13419444	0.81[ASN][1000 genomes]
rs13420171	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13425247	1.00[CHB][hapmap]
rs13427723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13428613	0.81[ASN][1000 genomes]
rs13432325	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13432813	0.81[ASN][1000 genomes]
rs1344236	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1344237	1.00[CHB][hapmap]
rs1529378	1.00[CHB][hapmap]
rs1529391	1.00[CHB][hapmap]
rs16859066	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs17282929	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs2033160	1.00[CHB][hapmap]
rs2052808	1.00[CHB][hapmap]
rs2081715	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2114596	0.81[ASN][1000 genomes]
rs2195072	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2217154	0.81[ASN][1000 genomes]
rs2356607	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2356608	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2555922	1.00[CHB][hapmap]
rs2557794	1.00[CHB][hapmap]
rs2676131	1.00[CHB][hapmap]
rs2676151	1.00[CHB][hapmap]
rs2723241	1.00[CHB][hapmap]
rs2723242	0.90[ASN][1000 genomes]
rs28740798	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34005022	0.82[EUR][1000 genomes]
rs34017170	0.86[EUR][1000 genomes]
rs34143031	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34303929	0.90[ASN][1000 genomes]
rs34453397	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34563349	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34622740	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34960296	0.90[ASN][1000 genomes]
rs35047553	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35112379	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35173138	0.81[ASN][1000 genomes]
rs35279794	0.87[EUR][1000 genomes]
rs35312173	0.81[ASN][1000 genomes]
rs35332006	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35381957	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35864840	0.87[EUR][1000 genomes]
rs35987434	0.85[EUR][1000 genomes]
rs35988467	0.81[ASN][1000 genomes]
rs3755121	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3770423	1.00[CHB][hapmap]
rs3770428	1.00[CHB][hapmap]
rs3770433	1.00[CHB][hapmap]
rs3770440	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs4564745	1.00[CHB][hapmap]
rs4668355	1.00[CHB][hapmap]
rs4668368	1.00[CHB][hapmap]
rs5028603	1.00[CHB][hapmap]
rs55758155	0.81[ASN][1000 genomes]
rs55987132	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56114146	0.95[EUR][1000 genomes]
rs56405950	0.81[ASN][1000 genomes]
rs57236236	0.90[ASN][1000 genomes]
rs6433276	1.00[CHB][hapmap]
rs6709077	0.87[EUR][1000 genomes]
rs6710035	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714164	1.00[CHB][hapmap]
rs6716127	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6730417	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6733178	1.00[CHB][hapmap]
rs6754315	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6757510	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6758331	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6761642	1.00[CHB][hapmap]
rs6761759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6761889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs719548	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72886381	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73013441	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7568083	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7579424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580629	1.00[CHB][hapmap]
rs7581195	0.81[ASN][1000 genomes]
rs7585619	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7587244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7593186	0.90[ASN][1000 genomes]
rs7593193	1.00[CHB][hapmap]
rs7594177	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7603316	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7603460	0.81[ASN][1000 genomes]
rs7603858	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7606502	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs7606822	1.00[CHB][hapmap]
rs9646785	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834456	chr2:171874210-172014659	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12692962	TLK1	cis	lesional skin	skin_eQTL
rs12692962	TLK1	cis	uninvolved skin	skin_eQTL
rs12692962	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs12692962	TLK1	cis	normal skin	skin_eQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171957200-172010400	Weak transcription	HSMM	muscle
2	chr2:171973600-172011000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:171985600-172006200	Weak transcription	Esophagus	oesophagus
4	chr2:171988200-172014400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:171989400-172007000	Weak transcription	Lung	lung
6	chr2:171990000-172016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:171990600-172004800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:171994000-172010400	Weak transcription	Thymus	Thymus
9	chr2:171994200-172010400	Weak transcription	Ovary	ovary
10	chr2:171994800-172005400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:171995200-172004400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:171995400-172012200	Weak transcription	Dnd41	blood
13	chr2:171996600-172006000	Weak transcription	Gastric	stomach
14	chr2:171996600-172015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:171996600-172015400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:171996600-172015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:171997000-172007600	Weak transcription	Placenta	Placenta
18	chr2:171997000-172010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:171998200-172003400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:171998200-172003600	Weak transcription	Brain Angular Gyrus	brain
21	chr2:171998200-172004800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:171998200-172007200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:171998200-172010400	Weak transcription	Psoas Muscle	Psoas
24	chr2:171998400-172004600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:171998400-172014800	Weak transcription	Brain Anterior Caudate	brain
26	chr2:171998600-172004000	Weak transcription	Fetal Stomach	stomach
27	chr2:171999000-172014800	Weak transcription	Osteobl	bone
28	chr2:171999200-172014000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:171999600-172004200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:171999600-172004800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:171999600-172012200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:171999600-172013800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:171999800-172003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:171999800-172004000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:171999800-172006000	Weak transcription	Small Intestine	intestine
36	chr2:172000000-172010400	Weak transcription	Spleen	Spleen
37	chr2:172000200-172003600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr2:172000200-172014600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:172000600-172003400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr2:172001000-172003400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:172001000-172005000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:172001000-172010800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:172001400-172003600	Enhancers	Primary T cells from cord blood	blood
44	chr2:172001600-172010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:172001800-172004600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:172001800-172006200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:172002000-172007600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:172002200-172003600	Enhancers	HMEC	breast
49	chr2:172002200-172004200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr2:172002200-172004200	Enhancers	Rectal Mucosa Donor 31	rectum

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