Variant report

Variant	rs13410683
Chromosome Location	chr2:171973722-171973723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171973244..171979114-chr2:171979690..171986296,7	K562	blood:
2	chr2:171962487..171964028-chr2:171970990..171973892,2	MCF-7	breast:
3	chr2:171942106..171944844-chr2:171973253..171975943,2	MCF-7	breast:

Extended variants
information (count: 173 )
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];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10177560	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10182205	0.94[EUR][1000 genomes]
rs10183486	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs10183909	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10186343	0.93[EUR][1000 genomes]
rs10191270	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10198197	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10199500	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10204062	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10208271	0.94[EUR][1000 genomes]
rs10208341	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10210693	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs10210791	0.93[EUR][1000 genomes]
rs10210883	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1025240	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs1025241	0.93[EUR][1000 genomes]
rs1035825	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1035827	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1035828	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];0.94[EUR][1000 genomes]
rs10930456	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10930457	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs11674590	0.91[EUR][1000 genomes]
rs11696064	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11899305	0.85[EUR][1000 genomes]
rs12053543	0.85[EUR][1000 genomes]
rs12467411	0.90[CHB][hapmap]
rs12473741	0.90[CHB][hapmap]
rs12477649	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12612871	0.92[CEU][hapmap]
rs12614580	0.90[EUR][1000 genomes]
rs12618232	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12618898	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12624094	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12988738	0.85[EUR][1000 genomes]
rs13004273	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13008199	0.96[CEU][hapmap]
rs13010307	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs13025198	0.93[EUR][1000 genomes]
rs13026662	0.81[EUR][1000 genomes]
rs13030784	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs13034529	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs13036123	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs13395669	0.93[EUR][1000 genomes]
rs13401706	0.95[EUR][1000 genomes]
rs13402107	0.93[EUR][1000 genomes]
rs13403285	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs13411575	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs13419444	0.94[EUR][1000 genomes]
rs13425247	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs13427723	0.94[EUR][1000 genomes]
rs13428613	0.94[EUR][1000 genomes]
rs13430489	0.94[EUR][1000 genomes]
rs13432813	0.94[EUR][1000 genomes]
rs1344237	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs1529378	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1529391	0.96[CEU][hapmap]
rs16859050	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16859081	0.85[EUR][1000 genomes]
rs16859142	0.92[EUR][1000 genomes]
rs16859157	0.91[CHB][hapmap]
rs17283147	0.84[EUR][1000 genomes]
rs17505447	0.81[CHB][hapmap]
rs1863679	0.85[CHB][hapmap]
rs1962841	0.85[EUR][1000 genomes]
rs1978592	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1989613	0.85[CHB][hapmap]
rs2010114	0.85[EUR][1000 genomes]
rs2033160	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2052808	0.84[EUR][1000 genomes]
rs2059723	0.85[CHB][hapmap]
rs2059724	0.85[EUR][1000 genomes]
rs2081715	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2081767	0.85[CHB][hapmap]
rs2081768	0.85[CHB][hapmap]
rs2098999	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2114595	0.84[EUR][1000 genomes]
rs2114596	0.94[EUR][1000 genomes]
rs2195116	0.84[CEU][hapmap]
rs2195117	0.89[EUR][1000 genomes]
rs2217154	0.94[EUR][1000 genomes]
rs2356423	0.83[EUR][1000 genomes]
rs2356593	0.86[EUR][1000 genomes]
rs2356597	0.86[EUR][1000 genomes]
rs2356599	0.92[EUR][1000 genomes]
rs2356608	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2555922	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2557794	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2557799	0.84[EUR][1000 genomes]
rs2676131	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2676151	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2723233	0.86[EUR][1000 genomes]
rs34004615	0.84[EUR][1000 genomes]
rs34518725	0.93[EUR][1000 genomes]
rs34792013	0.86[EUR][1000 genomes]
rs35173138	0.94[EUR][1000 genomes]
rs35312173	0.92[EUR][1000 genomes]
rs35988467	0.92[EUR][1000 genomes]
rs36058634	0.86[EUR][1000 genomes]
rs3731990	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731991	0.84[EUR][1000 genomes]
rs3731993	0.91[CHB][hapmap]
rs3755121	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3755124	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3755126	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3770419	0.86[CHB][hapmap]
rs3770423	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3770428	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs3770433	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs3770435	0.87[EUR][1000 genomes]
rs3770438	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4544401	0.82[EUR][1000 genomes]
rs4564745	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs4667673	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.86[EUR][1000 genomes]
rs4668343	0.89[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];0.86[EUR][1000 genomes]
rs5028603	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs55758155	0.94[EUR][1000 genomes]
rs55996750	0.89[EUR][1000 genomes]
rs56402728	0.94[EUR][1000 genomes]
rs56405950	0.93[EUR][1000 genomes]
rs6433276	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6711287	0.86[EUR][1000 genomes]
rs6714164	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6715332	0.84[EUR][1000 genomes]
rs6716127	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6722537	0.91[EUR][1000 genomes]
rs6730417	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6732229	0.93[EUR][1000 genomes]
rs6733178	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6734542	0.91[EUR][1000 genomes]
rs6734903	0.85[EUR][1000 genomes]
rs6742797	0.92[CEU][hapmap]
rs6742854	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6743201	0.85[EUR][1000 genomes]
rs6749427	0.90[EUR][1000 genomes]
rs6750849	0.91[EUR][1000 genomes]
rs6754315	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6761596	0.93[EUR][1000 genomes]
rs6761642	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs728455	0.82[ASN][1000 genomes]
rs731693	0.92[CEU][hapmap]
rs7421377	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs754058	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7560360	0.82[ASN][1000 genomes]
rs7578491	0.93[EUR][1000 genomes]
rs7580629	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs7581195	0.94[EUR][1000 genomes]
rs7581314	0.90[EUR][1000 genomes]
rs7582822	0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs7585418	0.90[EUR][1000 genomes]
rs7593193	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7594071	0.81[ASN][1000 genomes]
rs7597940	0.88[EUR][1000 genomes]
rs7600914	0.84[EUR][1000 genomes]
rs7603316	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs7603340	0.84[EUR][1000 genomes]
rs7603460	0.94[EUR][1000 genomes]
rs7606502	0.84[CEU][hapmap];0.94[EUR][1000 genomes]
rs7606822	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs930035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs930036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs958183	0.92[EUR][1000 genomes]
rs960222	0.84[EUR][1000 genomes]
rs964172	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]

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
rs13410683	TLK1	cis	uninvolved skin	skin_eQTL
rs13410683	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs13410683	TLK1	cis	lesional skin	skin_eQTL
rs13410683	TLK1	cis	normal skin	skin_eQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171900400-171975400	Weak transcription	Aorta	Aorta
2	chr2:171917000-172000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:171933200-171981000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:171943400-171973800	Weak transcription	NH-A	brain
5	chr2:171944800-171977400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:171950600-171991200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:171954600-171987200	Weak transcription	Fetal Stomach	stomach
8	chr2:171955800-171980800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:171956400-171980200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:171957000-171975400	Weak transcription	Right Ventricle	heart
11	chr2:171957200-171973800	Weak transcription	Esophagus	oesophagus
12	chr2:171957200-171975800	Weak transcription	Fetal Lung	lung
13	chr2:171957200-171976200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:171957200-171977800	Weak transcription	Thymus	Thymus
15	chr2:171957200-171978000	Weak transcription	NHEK	skin
16	chr2:171957200-171980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:171957200-171980000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:171957200-171982400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:171957200-171986000	Weak transcription	Spleen	Spleen
20	chr2:171957200-172010400	Weak transcription	HSMM	muscle
21	chr2:171957400-171975800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:171957600-171975400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:171959600-171975800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:171959600-171980000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:171961600-171975400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:171963800-171975600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:171965800-171974400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:171966600-171975400	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:171966600-171981200	Weak transcription	Brain Anterior Caudate	brain
30	chr2:171966800-171975600	Weak transcription	HMEC	breast
31	chr2:171967000-171974400	Weak transcription	HSMMtube	muscle
32	chr2:171967000-171975400	Weak transcription	Psoas Muscle	Psoas
33	chr2:171967000-171977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:171967000-171980000	Weak transcription	Pancreas	Pancrea
35	chr2:171967800-171974200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:171968200-171975200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:171968400-171981800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:171968800-171975200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:171968800-171985400	Weak transcription	Left Ventricle	heart
40	chr2:171969000-171974600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:171969400-171981000	Weak transcription	NHDF-Ad	bronchial
42	chr2:171969600-171974200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:171969600-171975400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:171969600-171975600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:171969800-171975200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:171970000-171974200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:171970200-171974200	Strong transcription	GM12878-XiMat	blood
48	chr2:171970200-171974600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:171970200-171975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:171970400-171975800	Weak transcription	Fetal Kidney	kidney

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