Variant report

Variant	rs16859066
Chromosome Location	chr2:171808625-171808626
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:171807824-171809104	K562	blood:	n/a	n/a
2	POLR2A	chr2:171808292-171813183	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171807096..171809968-chr2:171810006..171812450,2	MCF-7	breast:

Variant related genes	Relation type
GORASP2	TF binding region
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10183486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10189480	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs10191270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10198197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10199500	1.00[CHB][hapmap]
rs10207361	1.00[CHB][hapmap]
rs10208341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10210693	1.00[CHB][hapmap]
rs10210883	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1025240	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1035825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1035826	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs1035828	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1045327	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10515934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803853	0.94[ASN][1000 genomes]
rs10803854	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10930448	1.00[ASN][1000 genomes]
rs10930449	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10930453	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930456	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12151587	0.86[ASN][1000 genomes]
rs12471930	1.00[ASN][1000 genomes]
rs12612871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12692962	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs12988738	0.88[ASN][1000 genomes]
rs12996518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997252	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12998296	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13000644	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13000898	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13001088	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13002517	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs13003218	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs13004273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13007415	0.81[EUR][1000 genomes]
rs13008199	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13010307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13011011	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015226	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13016705	1.00[CHB][hapmap]
rs13026662	0.94[ASN][1000 genomes]
rs13028857	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13030784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13034529	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13035460	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13036123	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13402107	1.00[CHB][hapmap]
rs13403285	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13411575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13425247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13427723	1.00[CHB][hapmap]
rs1344237	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1529378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1529391	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16859081	0.91[ASN][1000 genomes]
rs17281735	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978592	1.00[JPT][hapmap]
rs1991370	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2033160	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2052808	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2081715	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2114738	0.94[ASN][1000 genomes]
rs2195116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2356607	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2356608	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2555922	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2557794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2557799	0.94[ASN][1000 genomes]
rs2676131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2676151	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2723241	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34004615	0.91[ASN][1000 genomes]
rs34005022	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34017170	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34330182	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34342928	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34532258	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34911788	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34960296	0.82[AMR][1000 genomes]
rs35123411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230775	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35279794	0.82[EUR][1000 genomes]
rs35864840	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35890547	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35900609	0.80[AMR][1000 genomes]
rs35987434	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3755125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770428	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770433	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770435	0.86[ASN][1000 genomes]
rs3770440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770441	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770442	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821090	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4564745	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4668349	0.89[ASN][1000 genomes]
rs4668350	0.89[ASN][1000 genomes]
rs4668355	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4668368	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5028603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6433267	0.94[ASN][1000 genomes]
rs6433276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6709077	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6710035	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs6714164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6714300	1.00[ASN][1000 genomes]
rs6715386	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6716127	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6724493	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6729847	0.94[ASN][1000 genomes]
rs6730417	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6733178	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6734903	0.91[ASN][1000 genomes]
rs6742797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6743201	0.91[ASN][1000 genomes]
rs6754315	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6757510	0.81[EUR][1000 genomes]
rs6758331	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6761642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6761759	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6761889	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs71415229	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71415231	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71415232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71415233	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71415235	0.80[AMR][1000 genomes]
rs72886381	0.81[EUR][1000 genomes]
rs731692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73976229	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570701	1.00[ASN][1000 genomes]
rs7579424	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs7580629	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7587244	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs7593186	0.82[AMR][1000 genomes]
rs7593193	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7603316	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7606502	1.00[CHB][hapmap]
rs7606822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs960222	0.86[ASN][1000 genomes]
rs965518	0.94[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
rs16859066	TLK1	cis	uninvolved skin	skin_eQTL
rs16859066	TLK1	cis	normal skin	skin_eQTL
rs16859066	TLK1	cis	lesional skin	skin_eQTL
rs16859066	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171787000-171810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:171787400-171810000	Weak transcription	Small Intestine	intestine
3	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
4	chr2:171787800-171809200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:171789600-171810000	Weak transcription	Stomach Mucosa	stomach
6	chr2:171794200-171809200	Weak transcription	Pancreas	Pancrea
7	chr2:171797000-171830600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:171800000-171809000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:171800600-171809200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:171803600-171824600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:171803800-171824400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:171803800-171825600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr2:171804000-171825000	Strong transcription	HepG2	liver
14	chr2:171804600-171808800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:171804600-171817400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:171804800-171824800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:171804800-171825800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:171805000-171817400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:171805000-171819600	Strong transcription	K562	blood
20	chr2:171805000-171824800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:171805000-171825000	Strong transcription	Dnd41	blood
22	chr2:171805200-171824800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:171805400-171812800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr2:171805400-171814000	Strong transcription	HUVEC	blood vessel
25	chr2:171805400-171814800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:171805400-171816400	Strong transcription	NHEK	skin
27	chr2:171805400-171824600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:171805400-171825000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:171805400-171825200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:171805400-171825400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:171805400-171825600	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr2:171805400-171825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:171805400-171825800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:171805600-171812800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:171805600-171813400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:171805600-171814600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:171805600-171815200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:171805600-171816600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:171805600-171817400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:171805600-171821800	Strong transcription	HSMM	muscle
41	chr2:171805600-171824600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:171805600-171824600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:171805600-171825800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr2:171805800-171813200	Strong transcription	HMEC	breast
45	chr2:171805800-171818400	Strong transcription	Adipose Nuclei	Adipose
46	chr2:171805800-171821800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:171805800-171823800	Strong transcription	NHDF-Ad	bronchial
48	chr2:171805800-171825200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr2:171805800-171825800	Strong transcription	Placenta	Placenta
50	chr2:171805800-171825800	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links