Variant report

Variant	rs964172
Chromosome Location	chr2:171935729-171935730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171933685..171936643-chr2:172289077..172291216,2	K562	blood:
2	chr2:171923456..171926638-chr2:171934420..171937360,3	K562	blood:
3	chr2:171934929..171937323-chr2:171937845..171939440,2	K562	blood:
4	chr2:171935229..171937932-chr2:172015681..172018523,3	MCF-7	breast:
5	chr2:171933890..171935925-chr2:171936259..171938371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 174 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs10171850	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10177560	0.92[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10182205	0.93[EUR][1000 genomes]
rs10183486	0.88[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs10183909	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10186343	0.94[EUR][1000 genomes]
rs10191270	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10198197	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10199500	0.96[CEU][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs10204062	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10208271	0.92[EUR][1000 genomes]
rs10208341	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10210693	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs10210791	0.92[EUR][1000 genomes]
rs10210883	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1025240	0.92[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1025241	0.92[EUR][1000 genomes]
rs1035825	0.96[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1035827	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1035828	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10803854	0.92[CEU][hapmap]
rs10803855	0.92[EUR][1000 genomes]
rs10930449	0.92[CEU][hapmap]
rs10930453	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10930455	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10930456	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10930457	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11674590	0.92[EUR][1000 genomes]
rs11696064	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11899305	0.86[EUR][1000 genomes]
rs11902369	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11904750	0.81[CHB][hapmap]
rs12053543	0.86[EUR][1000 genomes]
rs12467411	0.86[CHB][hapmap]
rs12473741	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs12477649	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12612871	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs12614580	0.91[EUR][1000 genomes]
rs12618232	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618898	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12624094	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12988738	0.85[EUR][1000 genomes]
rs13004273	0.96[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs13008199	0.96[CEU][hapmap];0.97[TSI][hapmap]
rs13010307	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13025198	0.94[EUR][1000 genomes]
rs13026662	0.81[EUR][1000 genomes]
rs13030784	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13034529	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13036123	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs13395669	0.90[EUR][1000 genomes]
rs13401706	0.92[EUR][1000 genomes]
rs13402107	0.92[EUR][1000 genomes]
rs13403285	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs13410683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13411575	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13419444	0.93[EUR][1000 genomes]
rs13425247	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13427723	0.92[EUR][1000 genomes]
rs13428613	0.92[EUR][1000 genomes]
rs13430489	0.93[EUR][1000 genomes]
rs13432813	0.92[EUR][1000 genomes]
rs1344237	0.92[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1529378	0.96[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1529391	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs16859050	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs16859081	0.86[EUR][1000 genomes]
rs16859142	0.94[EUR][1000 genomes]
rs16859157	0.86[CHB][hapmap]
rs17283147	0.84[EUR][1000 genomes]
rs17505447	0.81[CHB][hapmap]
rs1863679	0.82[CHB][hapmap]
rs1962841	0.86[EUR][1000 genomes]
rs1978592	0.96[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1989613	0.82[CHB][hapmap]
rs2010114	0.86[EUR][1000 genomes]
rs2033160	0.84[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs2052808	0.85[EUR][1000 genomes]
rs2059723	0.81[CHB][hapmap]
rs2059724	0.85[EUR][1000 genomes]
rs2081715	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2081767	0.81[CHB][hapmap]
rs2081768	0.81[CHB][hapmap]
rs2098999	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2114595	0.85[EUR][1000 genomes]
rs2114596	0.91[EUR][1000 genomes]
rs2195116	0.84[CEU][hapmap]
rs2195117	0.90[EUR][1000 genomes]
rs2217154	0.92[EUR][1000 genomes]
rs2356422	0.81[CHB][hapmap]
rs2356423	0.85[EUR][1000 genomes]
rs2356593	0.86[EUR][1000 genomes]
rs2356597	0.87[EUR][1000 genomes]
rs2356599	0.92[EUR][1000 genomes]
rs2356608	0.92[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2555922	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs2557794	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2557799	0.85[EUR][1000 genomes]
rs2676131	0.84[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2676151	0.96[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2723233	0.86[EUR][1000 genomes]
rs34004615	0.85[EUR][1000 genomes]
rs34518725	0.93[EUR][1000 genomes]
rs34792013	0.87[EUR][1000 genomes]
rs35173138	0.93[EUR][1000 genomes]
rs35312173	0.90[EUR][1000 genomes]
rs35988467	0.90[EUR][1000 genomes]
rs36058634	0.86[EUR][1000 genomes]
rs3731990	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3731991	0.85[EUR][1000 genomes]
rs3731993	0.86[CHB][hapmap]
rs3755121	0.96[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs3755124	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs3755126	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs3770419	0.82[CHB][hapmap]
rs3770423	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3770428	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs3770433	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs3770435	0.87[EUR][1000 genomes]
rs3770438	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs4544401	0.84[EUR][1000 genomes]
rs4564745	0.92[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs4667673	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668343	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4668354	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4668355	0.92[CEU][hapmap]
rs4668368	0.84[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs5028603	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs55758155	0.92[EUR][1000 genomes]
rs55996750	0.89[EUR][1000 genomes]
rs56402728	0.92[EUR][1000 genomes]
rs56405950	0.92[EUR][1000 genomes]
rs6433276	0.96[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6711287	0.87[EUR][1000 genomes]
rs6714164	0.92[CEU][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6715332	0.85[EUR][1000 genomes]
rs6716127	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6722537	0.92[EUR][1000 genomes]
rs6730417	0.96[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs6732229	0.94[EUR][1000 genomes]
rs6733178	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs6734542	0.92[EUR][1000 genomes]
rs6734903	0.86[EUR][1000 genomes]
rs6742797	0.92[CEU][hapmap]
rs6742854	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743201	0.86[EUR][1000 genomes]
rs6749427	0.92[EUR][1000 genomes]
rs6750849	0.92[EUR][1000 genomes]
rs6754315	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs6761596	0.94[EUR][1000 genomes]
rs6761642	0.96[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs731693	0.92[CEU][hapmap]
rs7421377	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754058	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs7578491	0.90[EUR][1000 genomes]
rs7580629	0.84[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7581195	0.91[EUR][1000 genomes]
rs7581314	0.87[EUR][1000 genomes]
rs7582822	0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs7585418	0.90[EUR][1000 genomes]
rs7593193	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs7597940	0.85[EUR][1000 genomes]
rs7600914	0.84[EUR][1000 genomes]
rs7603316	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs7603340	0.84[EUR][1000 genomes]
rs7603460	0.93[EUR][1000 genomes]
rs7606502	0.93[EUR][1000 genomes]
rs7606822	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs930035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958183	0.91[EUR][1000 genomes]
rs960222	0.84[EUR][1000 genomes]

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	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
2	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
rs964172	TLK1	cis	uninvolved skin	skin_eQTL
rs964172	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs964172	TLK1	cis	lesional skin	skin_eQTL
rs964172	TLK1	cis	normal skin	skin_eQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171841600-171940000	Weak transcription	Right Ventricle	heart
2	chr2:171878000-171943200	Weak transcription	Small Intestine	intestine
3	chr2:171878800-171940000	Weak transcription	Stomach Mucosa	stomach
4	chr2:171892400-171943400	Weak transcription	Spleen	Spleen
5	chr2:171898200-171946200	Weak transcription	Pancreas	Pancrea
6	chr2:171900000-171940000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:171900200-171936400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:171900200-171937800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:171900400-171975400	Weak transcription	Aorta	Aorta
10	chr2:171903000-171940000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:171905800-171939200	Weak transcription	HSMMtube	muscle
12	chr2:171907800-171942800	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:171911600-171943200	Weak transcription	NH-A	brain
14	chr2:171912400-171937400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:171916600-171940000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:171916600-171944600	Weak transcription	Lung	lung
17	chr2:171916600-171950200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:171916600-171970800	Weak transcription	Ovary	ovary
19	chr2:171916800-171942200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:171916800-171943200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:171917000-171937200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:171917000-171940400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:171917000-171942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:171917000-171942800	Weak transcription	Adipose Nuclei	Adipose
25	chr2:171917000-171942800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:171917000-171942800	Weak transcription	Gastric	stomach
27	chr2:171917000-171942800	Weak transcription	Left Ventricle	heart
28	chr2:171917000-171943000	Weak transcription	Osteobl	bone
29	chr2:171917000-171943200	Weak transcription	Fetal Lung	lung
30	chr2:171917000-171946200	Weak transcription	Psoas Muscle	Psoas
31	chr2:171917000-171948000	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:171917000-171953200	Weak transcription	HSMM	muscle
33	chr2:171917000-171956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:171917000-172000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:171917200-171937600	Weak transcription	HUVEC	blood vessel
36	chr2:171917400-171943200	Weak transcription	NHDF-Ad	bronchial
37	chr2:171917600-171942000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:171917800-171938200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:171918400-171940600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:171921000-171937200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:171921200-171938400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:171921400-171937800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:171924000-171940400	Weak transcription	Fetal Brain Male	brain
44	chr2:171924800-171939800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:171925800-171939000	Strong transcription	GM12878-XiMat	blood
46	chr2:171926400-171936200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:171926400-171938400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:171926400-171943200	Weak transcription	A549	lung
49	chr2:171927200-171938400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:171928200-171936600	Strong transcription	Fetal Thymus	thymus

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