Variant report

Variant	rs12471930
Chromosome Location	chr2:171792429-171792430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10183486	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs10189480	1.00[CHB][hapmap]
rs10191270	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10198197	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10207361	1.00[CHB][hapmap]
rs10208341	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10210693	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10210791	0.80[GIH][hapmap]
rs10210883	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1025240	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs1035825	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs1035826	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1035827	0.80[TSI][hapmap]
rs1035828	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs1045327	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10515934	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10803853	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10803854	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930448	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930449	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930453	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930455	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930457	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11696064	0.83[TSI][hapmap]
rs11902369	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12151587	0.86[ASN][1000 genomes]
rs12477649	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs12612871	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618898	0.87[CEU][hapmap];0.80[YRI][hapmap]
rs12988738	0.88[ASN][1000 genomes]
rs12996518	1.00[ASN][1000 genomes]
rs12997252	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12998296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13000898	0.91[ASN][1000 genomes]
rs13002517	1.00[CHB][hapmap]
rs13003218	1.00[CHB][hapmap]
rs13004273	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs13008199	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs13010307	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13011011	0.88[ASN][1000 genomes]
rs13015226	0.94[ASN][1000 genomes]
rs13016705	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13026662	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13028857	0.82[ASN][1000 genomes]
rs13030784	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13034529	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13035460	0.94[ASN][1000 genomes]
rs13036123	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13402107	1.00[CHB][hapmap]
rs13403285	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13410683	0.88[CEU][hapmap]
rs13411575	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13425247	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13427723	1.00[CHB][hapmap]
rs1344237	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs1529378	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs1529391	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859050	0.83[CEU][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs16859066	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16859081	0.91[ASN][1000 genomes]
rs17281735	1.00[ASN][1000 genomes]
rs1978592	0.92[CEU][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs1991370	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2033160	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs2052808	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2081715	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2098999	0.83[CEU][hapmap]
rs2114738	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2195116	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2356607	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2356608	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2555922	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2557794	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2557799	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2676131	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2676151	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2723241	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34004615	0.91[ASN][1000 genomes]
rs34005022	0.82[ASN][1000 genomes]
rs34017170	0.91[ASN][1000 genomes]
rs34330182	0.88[ASN][1000 genomes]
rs34342928	0.97[ASN][1000 genomes]
rs34532258	0.82[ASN][1000 genomes]
rs34911788	0.94[ASN][1000 genomes]
rs35123411	1.00[ASN][1000 genomes]
rs35230775	0.82[ASN][1000 genomes]
rs35864840	0.91[ASN][1000 genomes]
rs35890547	1.00[ASN][1000 genomes]
rs35987434	0.94[ASN][1000 genomes]
rs3755121	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs3755124	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs3755125	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3755126	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs3770423	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770428	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770433	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770435	0.86[ASN][1000 genomes]
rs3770438	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3770440	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3770441	0.94[ASN][1000 genomes]
rs3770442	1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs4564745	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs4667673	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs4668343	0.83[CEU][hapmap]
rs4668349	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4668350	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4668354	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4668355	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668368	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs5028603	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6433267	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs6709077	0.91[ASN][1000 genomes]
rs6710035	1.00[CHB][hapmap]
rs6714164	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs6714300	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715386	0.94[ASN][1000 genomes]
rs6716127	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs6724493	0.94[ASN][1000 genomes]
rs6729847	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6730417	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs6731774	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6733178	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6734903	0.91[ASN][1000 genomes]
rs6742564	0.88[EUR][1000 genomes]
rs6742797	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743201	0.91[ASN][1000 genomes]
rs6754315	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6758331	1.00[CHB][hapmap]
rs6760293	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6761642	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs6761759	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6761889	1.00[CHB][hapmap]
rs71415229	0.94[ASN][1000 genomes]
rs71415231	0.88[ASN][1000 genomes]
rs71415232	1.00[ASN][1000 genomes]
rs71415233	0.88[ASN][1000 genomes]
rs731692	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs731693	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976229	1.00[ASN][1000 genomes]
rs754058	0.87[YRI][hapmap]
rs7570701	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580629	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs7587244	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7593193	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7603316	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7606822	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs930035	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs930036	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs960222	0.86[ASN][1000 genomes]
rs964172	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs965518	0.91[EUR][1000 genomes];0.94[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	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12471930	TLK1	cis	uninvolved skin	skin_eQTL
rs12471930	TLK1	cis	lesional skin	skin_eQTL
rs12471930	DLX1	cis	cerebellum	SCAN
rs12471930	TLK1	cis	normal skin	skin_eQTL
rs12471930	GORASP2	cis	cerebellum	SCAN
rs12471930	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171787000-171793800	Weak transcription	Gastric	stomach
2	chr2:171787000-171810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:171787200-171793200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:171787200-171793800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:171787200-171795200	Weak transcription	Ovary	ovary
6	chr2:171787400-171792800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:171787400-171792800	Weak transcription	Spleen	Spleen
8	chr2:171787400-171793000	Weak transcription	Placenta	Placenta
9	chr2:171787400-171806000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:171787400-171806000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:171787400-171806000	Weak transcription	Esophagus	oesophagus
12	chr2:171787400-171806000	Weak transcription	Psoas Muscle	Psoas
13	chr2:171787400-171807200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:171787400-171808200	Weak transcription	Aorta	Aorta
15	chr2:171787400-171810000	Weak transcription	Small Intestine	intestine
16	chr2:171787600-171793200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:171787600-171793800	Weak transcription	Right Ventricle	heart
18	chr2:171787600-171796600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:171787600-171806800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:171787600-171807600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
22	chr2:171787800-171795000	Weak transcription	Adipose Nuclei	Adipose
23	chr2:171787800-171795800	Weak transcription	Primary B cells from cord blood	blood
24	chr2:171787800-171798800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:171787800-171806000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:171787800-171806000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:171787800-171806200	Weak transcription	Fetal Kidney	kidney
28	chr2:171787800-171806600	Weak transcription	Fetal Brain Female	brain
29	chr2:171787800-171807000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:171787800-171807400	Weak transcription	Brain Germinal Matrix	brain
31	chr2:171787800-171809200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:171788000-171793000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:171788000-171793000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:171788000-171794200	Weak transcription	HMEC	breast
35	chr2:171788000-171794400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:171788000-171805800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:171788000-171806000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:171788000-171806000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:171788000-171806200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:171788000-171806600	Weak transcription	Fetal Lung	lung
41	chr2:171788000-171806800	Weak transcription	Brain Anterior Caudate	brain
42	chr2:171788000-171806800	Weak transcription	A549	lung
43	chr2:171788000-171807600	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:171788000-171808400	Weak transcription	Brain Angular Gyrus	brain
45	chr2:171788200-171795600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:171788200-171806200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:171788400-171793200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:171788400-171805400	Weak transcription	HUVEC	blood vessel
49	chr2:171788400-171805600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:171788400-171806200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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