Variant report

Variant	rs10191270
Chromosome Location	chr2:171990516-171990517
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 168 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10171850	0.96[CEU][hapmap]
rs10177560	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10182205	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10183486	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10186343	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10189480	1.00[CHB][hapmap]
rs10198197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10199500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10207361	1.00[CHB][hapmap]
rs10208271	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10208341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10210693	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10210791	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10210883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1025240	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1025241	0.90[EUR][1000 genomes]
rs1035825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1035826	1.00[CHB][hapmap]
rs1035827	0.88[CEU][hapmap]
rs1035828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1045327	1.00[CHB][hapmap]
rs10515934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10803854	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10803855	0.89[EUR][1000 genomes]
rs10930449	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10930455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10930456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10930457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11674590	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11696064	0.83[CEU][hapmap]
rs11899305	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12053543	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12477649	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12612871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12614580	0.86[EUR][1000 genomes]
rs12618898	0.92[CEU][hapmap]
rs12692962	1.00[CHB][hapmap]
rs12988738	0.81[EUR][1000 genomes]
rs12997252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12998296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13002517	1.00[CHB][hapmap]
rs13003218	1.00[CHB][hapmap]
rs13004273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs13008199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13010307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13016705	1.00[CHB][hapmap]
rs13025198	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13030784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13034529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13036123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13395669	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13401706	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13402107	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13403285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13410683	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13411575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13419444	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13425247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13427723	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13428613	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13430489	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13432813	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1344237	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1529378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1529391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16859066	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16859081	0.81[EUR][1000 genomes]
rs16859142	0.89[EUR][1000 genomes]
rs17283147	0.81[EUR][1000 genomes]
rs1962841	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1978592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1991370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2010114	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2033160	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2052808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2059724	0.82[EUR][1000 genomes]
rs2081715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2114595	0.82[EUR][1000 genomes]
rs2114596	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2195072	1.00[CHB][hapmap]
rs2195117	0.86[EUR][1000 genomes]
rs2217154	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2356593	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2356597	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2356599	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2356607	1.00[CHB][hapmap]
rs2356608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2555922	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2557794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2557799	0.80[EUR][1000 genomes]
rs2676131	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2676151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2723233	0.83[EUR][1000 genomes]
rs2723241	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34004615	0.80[EUR][1000 genomes]
rs34518725	0.90[EUR][1000 genomes]
rs34792013	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35173138	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35312173	0.89[EUR][1000 genomes]
rs35988467	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36058634	0.83[EUR][1000 genomes]
rs3731991	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3755121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3770423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3770428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs3770433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770435	0.83[EUR][1000 genomes]
rs3770438	0.91[CEU][hapmap]
rs3770440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4564745	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4667673	0.96[CEU][hapmap]
rs4668354	0.96[CEU][hapmap]
rs4668355	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4668368	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5028603	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs55758155	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55996750	0.86[EUR][1000 genomes]
rs56402728	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56405950	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6433276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6710035	1.00[CHB][hapmap]
rs6711287	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6714164	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6715332	0.81[EUR][1000 genomes]
rs6716127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6722537	0.88[EUR][1000 genomes]
rs6730417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6732229	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6733178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6734542	0.88[EUR][1000 genomes]
rs6734903	0.81[EUR][1000 genomes]
rs6742797	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6743201	0.81[EUR][1000 genomes]
rs6749427	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6750849	0.88[EUR][1000 genomes]
rs6754315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6758331	1.00[CHB][hapmap]
rs6761596	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6761642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6761759	1.00[CHB][hapmap]
rs6761889	1.00[CHB][hapmap]
rs719548	1.00[CHB][hapmap]
rs731692	1.00[CHB][hapmap]
rs731693	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7421377	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7578491	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7579424	1.00[CHB][hapmap]
rs7580629	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7581195	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7581314	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7585418	0.87[EUR][1000 genomes]
rs7587244	1.00[CHB][hapmap]
rs7593193	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7597940	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7600914	0.81[EUR][1000 genomes]
rs7603316	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7603340	0.81[EUR][1000 genomes]
rs7603460	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606502	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs930035	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs930036	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs958183	0.89[EUR][1000 genomes]
rs964172	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9646785	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv2275161	chr2:171990515-171990517	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10191270	TLK1	cis	uninvolved skin	skin_eQTL
rs10191270	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs10191270	TLK1	cis	lesional skin	skin_eQTL
rs10191270	TLK1	cis	normal skin	skin_eQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171917000-172000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:171950600-171991200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:171957200-172010400	Weak transcription	HSMM	muscle
4	chr2:171971200-171993000	Weak transcription	Gastric	stomach
5	chr2:171973600-172011000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:171974000-171996400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:171974000-172003200	Weak transcription	Fetal Intestine Small	intestine
8	chr2:171974000-172003200	Weak transcription	Fetal Thymus	thymus
9	chr2:171974200-171993600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:171974200-171996400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:171974200-172002400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:171974400-171992400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:171974400-172003200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:171976400-171993400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:171982000-171991600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:171982000-171993400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:171982200-171993000	Weak transcription	Small Intestine	intestine
18	chr2:171984600-172003000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:171985600-172006200	Weak transcription	Esophagus	oesophagus
20	chr2:171986400-171995800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:171986400-171996400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:171987200-171993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:171987400-171993400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:171987400-171999400	Weak transcription	Spleen	Spleen
25	chr2:171987600-171993000	Weak transcription	Stomach Mucosa	stomach
26	chr2:171988000-171991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:171988200-172014400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:171988400-171999800	Enhancers	HepG2	liver
29	chr2:171988600-171990800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr2:171988600-171990800	Enhancers	Pancreas	Pancrea
31	chr2:171988600-171990800	Enhancers	Psoas Muscle	Psoas
32	chr2:171988800-171990600	Enhancers	H9 Cell Line	embryonic stem cell
33	chr2:171988800-171991200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr2:171989000-171991800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:171989200-171991200	Enhancers	K562	blood
36	chr2:171989200-171996600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:171989400-171991200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:171989400-171991200	Weak transcription	A549	lung
39	chr2:171989400-171991600	Enhancers	Liver	Liver
40	chr2:171989400-171993400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:171989400-171994000	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:171989400-172007000	Weak transcription	Lung	lung
43	chr2:171989800-171991200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:171989800-171991800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:171989800-171991800	Weak transcription	Osteobl	bone
46	chr2:171989800-171996800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:171990000-171991400	Enhancers	GM12878-XiMat	blood
48	chr2:171990000-171993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:171990000-171993400	Weak transcription	Placenta	Placenta
50	chr2:171990000-171993400	Weak transcription	Right Atrium	heart

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