Variant report

Variant	rs4667673
Chromosome Location	chr2:171843415-171843416
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171829711..171831608-chr2:171843095..171845582,2	K562	blood:
2	chr2:171843371..171845659-chr2:172015134..172017450,3	MCF-7	breast:
3	chr2:171843140..171844937-chr2:171867399..171870278,2	K562	blood:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10171850	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10177560	0.88[CEU][hapmap]
rs10182205	0.81[EUR][1000 genomes]
rs10183486	0.84[CEU][hapmap]
rs10186343	0.82[EUR][1000 genomes]
rs10191270	0.96[CEU][hapmap]
rs10198197	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10199500	0.92[CEU][hapmap]
rs10208271	0.81[EUR][1000 genomes]
rs10208341	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10210693	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10210791	0.80[EUR][1000 genomes]
rs10210883	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1025240	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1025241	0.80[EUR][1000 genomes]
rs1035825	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1035827	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10803854	0.88[CEU][hapmap]
rs10803855	0.84[EUR][1000 genomes]
rs10930449	0.88[CEU][hapmap]
rs10930453	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10930455	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10930456	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10930457	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11674590	0.84[EUR][1000 genomes]
rs11696064	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11902369	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs12467411	0.82[CHB][hapmap]
rs12473741	0.86[CHB][hapmap]
rs12477649	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs12612871	0.88[CEU][hapmap];0.93[YRI][hapmap]
rs12614580	0.84[EUR][1000 genomes]
rs12618232	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12618898	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12624094	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12988738	0.87[EUR][1000 genomes]
rs13004273	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13008199	0.92[CEU][hapmap]
rs13010307	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13025198	0.82[EUR][1000 genomes]
rs13026662	0.84[EUR][1000 genomes]
rs13030784	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13034529	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13036123	0.95[CEU][hapmap]
rs13401706	0.81[EUR][1000 genomes]
rs13402107	0.80[EUR][1000 genomes]
rs13403285	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs13410683	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.86[EUR][1000 genomes]
rs13411575	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13419444	0.81[EUR][1000 genomes]
rs13425247	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13427723	0.81[EUR][1000 genomes]
rs13428613	0.81[EUR][1000 genomes]
rs13430489	0.81[EUR][1000 genomes]
rs13432813	0.81[EUR][1000 genomes]
rs1344237	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1529378	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1529391	0.92[CEU][hapmap]
rs16859050	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs16859081	0.89[EUR][1000 genomes]
rs16859142	0.81[EUR][1000 genomes]
rs16859157	0.83[CHB][hapmap]
rs1978592	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2033160	0.81[CEU][hapmap]
rs2059724	0.85[EUR][1000 genomes]
rs2081715	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2098999	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap]
rs2195116	0.80[CEU][hapmap]
rs2195117	0.85[EUR][1000 genomes]
rs2217154	0.81[EUR][1000 genomes]
rs2356423	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2356608	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2555922	0.80[CEU][hapmap]
rs2557794	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2557799	0.88[EUR][1000 genomes]
rs2676131	0.81[CEU][hapmap]
rs2676151	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs34004615	0.90[EUR][1000 genomes]
rs34518725	0.82[EUR][1000 genomes]
rs35173138	0.81[EUR][1000 genomes]
rs3731990	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3731993	0.83[CHB][hapmap]
rs3755121	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs3755124	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3755126	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3770423	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs3770428	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs3770433	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs3770435	0.87[EUR][1000 genomes]
rs3770438	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs4544401	0.91[EUR][1000 genomes]
rs4564745	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4668343	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap]
rs4668354	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs4668355	0.88[CEU][hapmap]
rs4668368	0.81[CEU][hapmap]
rs5028603	0.81[CEU][hapmap]
rs55758155	0.81[EUR][1000 genomes]
rs55996750	0.85[EUR][1000 genomes]
rs56402728	0.81[EUR][1000 genomes]
rs56405950	0.80[EUR][1000 genomes]
rs6433276	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6714164	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6715332	0.85[EUR][1000 genomes]
rs6716127	0.88[CEU][hapmap]
rs6722537	0.84[EUR][1000 genomes]
rs6730417	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6731774	0.88[ASN][1000 genomes]
rs6732229	0.82[EUR][1000 genomes]
rs6733178	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6734542	0.84[EUR][1000 genomes]
rs6734903	0.89[EUR][1000 genomes]
rs6742564	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6742797	0.88[CEU][hapmap]
rs6742854	0.81[EUR][1000 genomes]
rs6743201	0.89[EUR][1000 genomes]
rs6750849	0.84[EUR][1000 genomes]
rs6754315	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6761596	0.82[EUR][1000 genomes]
rs6761642	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs731693	0.88[CEU][hapmap]
rs7421377	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs754058	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs7580629	0.81[CEU][hapmap]
rs7582822	0.91[CHB][hapmap]
rs7585418	0.85[EUR][1000 genomes]
rs7593193	0.82[CEU][hapmap]
rs7603316	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7603460	0.81[EUR][1000 genomes]
rs7606502	0.81[EUR][1000 genomes]
rs7606822	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs930035	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs930036	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs960222	0.87[EUR][1000 genomes]
rs964172	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.81[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4667673	TLK1	cis	normal skin	skin_eQTL
rs4667673	TLK1	cis	lesional skin	skin_eQTL
rs4667673	TLK1	cis	uninvolved skin	skin_eQTL
rs4667673	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171830600-171902800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:171830800-171891400	Weak transcription	Spleen	Spleen
3	chr2:171831000-171847600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:171831000-171850000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:171831200-171845400	Weak transcription	HMEC	breast
6	chr2:171831200-171845800	Weak transcription	Osteobl	bone
7	chr2:171831200-171847000	Weak transcription	A549	lung
8	chr2:171831200-171857400	Weak transcription	HSMMtube	muscle
9	chr2:171831400-171849400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:171831400-171857000	Weak transcription	NHEK	skin
11	chr2:171831400-171879200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:171831400-171916200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:171832000-171844800	Weak transcription	GM12878-XiMat	blood
14	chr2:171832600-171846000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:171832600-171852200	Weak transcription	Fetal Intestine Small	intestine
16	chr2:171833000-171848800	Weak transcription	HepG2	liver
17	chr2:171836600-171844800	Weak transcription	Primary T cells from cord blood	blood
18	chr2:171837600-171849200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:171838400-171849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:171838600-171862000	Weak transcription	Ovary	ovary
21	chr2:171838800-171843800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:171838800-171845400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:171838800-171847600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:171838800-171861800	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:171839000-171852400	Weak transcription	NHLF	lung
26	chr2:171839200-171846600	Weak transcription	Liver	Liver
27	chr2:171839200-171847200	Weak transcription	K562	blood
28	chr2:171839200-171854800	Weak transcription	Pancreas	Pancrea
29	chr2:171839400-171844600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:171839600-171844600	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:171839800-171845600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:171840200-171845000	Weak transcription	Primary B cells from cord blood	blood
33	chr2:171840400-171843600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:171840400-171844600	Weak transcription	Fetal Stomach	stomach
35	chr2:171840400-171844800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:171840800-171845400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:171840800-171861800	Weak transcription	Small Intestine	intestine
38	chr2:171840800-171879200	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:171841000-171844800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:171841000-171845400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:171841000-171845400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:171841000-171845400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:171841000-171847200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:171841000-171848800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:171841000-171852400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:171841000-171862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:171841000-171865400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:171841000-171877800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:171841000-171895800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:171841200-171844200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links