Variant report

Variant	rs7421377
Chromosome Location	chr2:171996840-171996841
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171978962..171981952-chr2:171996224..171998701,2	K562	blood:
2	chr2:171830106..171833063-chr2:171996453..171998706,2	K562	blood:
3	chr2:171994040..171997027-chr2:172088765..172091455,2	K562	blood:

Extended variants
information (count: 163 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10171850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10177560	0.96[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10182205	0.94[EUR][1000 genomes]
rs10183486	0.92[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10183909	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10186343	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10191270	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs10198197	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs10199500	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10204062	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208271	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10208341	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs10210693	0.92[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10210791	0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10210883	0.92[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1025240	0.88[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1025241	0.93[EUR][1000 genomes]
rs1035825	0.92[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1035827	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1035828	0.84[EUR][1000 genomes]
rs10803854	0.88[CEU][hapmap]
rs10803855	0.92[EUR][1000 genomes]
rs10930449	0.88[CEU][hapmap]
rs10930453	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs10930455	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10930456	0.92[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10930457	0.92[CEU][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs11674590	0.91[EUR][1000 genomes]
rs11696064	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11899305	0.85[EUR][1000 genomes]
rs12053543	0.85[EUR][1000 genomes]
rs12467411	0.81[CHB][hapmap]
rs12473741	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs12477649	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12612871	0.88[CEU][hapmap]
rs12614580	0.90[EUR][1000 genomes]
rs12618232	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12618898	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12624094	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12988738	0.85[EUR][1000 genomes]
rs13004273	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13008199	0.92[CEU][hapmap]
rs13010307	0.92[CEU][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs13025198	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13026662	0.81[EUR][1000 genomes]
rs13030784	0.92[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13034529	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs13036123	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs13395669	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13401706	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13402107	0.93[EUR][1000 genomes]
rs13403285	0.89[CEU][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13410683	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]
rs13411575	0.92[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13419444	0.94[EUR][1000 genomes]
rs13425247	0.92[CEU][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs13427723	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13428613	0.94[EUR][1000 genomes]
rs13430489	0.94[EUR][1000 genomes]
rs13432813	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1344237	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1529378	0.92[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1529391	0.92[CEU][hapmap]
rs16859081	0.85[EUR][1000 genomes]
rs16859142	0.92[EUR][1000 genomes]
rs16859157	0.82[CHB][hapmap]
rs17283147	0.84[EUR][1000 genomes]
rs1863679	0.86[CHB][hapmap]
rs1962841	0.85[EUR][1000 genomes]
rs1978592	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1989613	0.86[CHB][hapmap]
rs2010114	0.85[EUR][1000 genomes]
rs2033160	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs2052808	0.84[EUR][1000 genomes]
rs2059724	0.85[EUR][1000 genomes]
rs2081715	0.92[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2114595	0.84[EUR][1000 genomes]
rs2114596	0.93[EUR][1000 genomes]
rs2195117	0.89[EUR][1000 genomes]
rs2217154	0.82[AFR][1000 genomes];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	0.96[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2555922	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs2557794	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2557799	0.84[EUR][1000 genomes]
rs2676131	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs2676151	0.92[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	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731991	0.84[EUR][1000 genomes]
rs3731993	0.82[CHB][hapmap]
rs3755121	0.92[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3770419	0.87[CHB][hapmap]
rs3770423	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs3770428	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs3770433	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs3770435	0.87[EUR][1000 genomes]
rs3770438	0.88[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4544401	0.82[EUR][1000 genomes]
rs4564745	0.96[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4667673	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs4668354	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4668355	0.88[CEU][hapmap]
rs4668368	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs5028603	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs55758155	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55996750	0.89[EUR][1000 genomes]
rs56402728	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56405950	0.93[EUR][1000 genomes]
rs6433276	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6433282	0.81[ASN][1000 genomes]
rs6711287	0.86[EUR][1000 genomes]
rs6714164	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6715332	0.84[EUR][1000 genomes]
rs6716127	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6722537	0.91[EUR][1000 genomes]
rs6730417	0.92[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6732229	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6733178	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs6734542	0.91[EUR][1000 genomes]
rs6734903	0.85[EUR][1000 genomes]
rs6742854	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6743201	0.85[EUR][1000 genomes]
rs6749427	0.90[EUR][1000 genomes]
rs6750849	0.91[EUR][1000 genomes]
rs6754315	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs6761596	0.93[EUR][1000 genomes]
rs6761642	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs728455	0.83[ASN][1000 genomes]
rs731693	0.88[CEU][hapmap]
rs754058	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7560360	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7578491	0.92[EUR][1000 genomes]
rs7580629	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs7581195	0.93[EUR][1000 genomes]
rs7581314	0.89[EUR][1000 genomes]
rs7582822	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585418	0.90[EUR][1000 genomes]
rs7593193	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs7594071	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7597940	0.87[EUR][1000 genomes]
rs7600914	0.84[EUR][1000 genomes]
rs7603316	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs7603340	0.84[EUR][1000 genomes]
rs7603460	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7606502	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs7606822	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs930035	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs930036	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs958183	0.92[EUR][1000 genomes]
rs960222	0.84[EUR][1000 genomes]
rs964172	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]

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
rs7421377	TLK1	cis	uninvolved skin	skin_eQTL
rs7421377	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs7421377	TLK1	cis	lesional skin	skin_eQTL
rs7421377	TLK1	cis	normal skin	skin_eQTL

Chromatin state (count:84 , 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	chr2:171957200-172010400	Weak transcription	HSMM	muscle
3	chr2:171973600-172011000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:171974000-172003200	Weak transcription	Fetal Intestine Small	intestine
5	chr2:171974000-172003200	Weak transcription	Fetal Thymus	thymus
6	chr2:171974200-172002400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:171974400-172003200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:171984600-172003000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:171985600-172006200	Weak transcription	Esophagus	oesophagus
10	chr2:171987400-171999400	Weak transcription	Spleen	Spleen
11	chr2:171988200-172014400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:171988400-171999800	Enhancers	HepG2	liver
13	chr2:171989400-172007000	Weak transcription	Lung	lung
14	chr2:171990000-172016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:171990200-171997400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:171990600-172004800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:171990800-172001200	Weak transcription	Primary B cells from cord blood	blood
18	chr2:171991200-171997400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:171991600-171998000	Weak transcription	Aorta	Aorta
20	chr2:171992200-171997200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:171992200-171999800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:171993600-171997600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:171993800-171997600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:171993800-171997600	Weak transcription	Small Intestine	intestine
25	chr2:171993800-172001800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:171994000-171997200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:171994000-172002200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:171994000-172010400	Weak transcription	Thymus	Thymus
29	chr2:171994200-171997800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:171994200-171997800	Weak transcription	Psoas Muscle	Psoas
31	chr2:171994200-171999000	Weak transcription	Stomach Mucosa	stomach
32	chr2:171994200-171999400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:171994200-172002800	Weak transcription	Right Atrium	heart
34	chr2:171994200-172010400	Weak transcription	Ovary	ovary
35	chr2:171994800-172005400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr2:171995000-172001000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr2:171995200-171997800	Weak transcription	Adipose Nuclei	Adipose
38	chr2:171995200-171997800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:171995200-171998200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr2:171995200-171999800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr2:171995200-172004400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:171995400-171997600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:171995400-171997600	Weak transcription	Primary T cells from cord blood	blood
44	chr2:171995400-171997800	Weak transcription	A549	lung
45	chr2:171995400-171998000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:171995400-172012200	Weak transcription	Dnd41	blood
47	chr2:171995600-171997600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:171995800-171997000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:171995800-171997000	Enhancers	Placenta	Placenta
50	chr2:171995800-171997000	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links