Variant report

Variant	rs16859081
Chromosome Location	chr2:171847832-171847833
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171846628..171848160-chr2:172015800..172017985,2	MCF-7	breast:
2	chr2:171846054..171849004-chr2:172014237..172017163,3	MCF-7	breast:
3	chr2:171847478..171849629-chr2:171852336..171855019,4	K562	blood:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 186 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:185)

rs_ID	r²[population]
rs10182205	0.90[EUR][1000 genomes]
rs10183486	0.87[EUR][1000 genomes]
rs10186343	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10191270	0.81[EUR][1000 genomes]
rs10198197	0.89[EUR][1000 genomes]
rs10208271	0.89[EUR][1000 genomes]
rs10208341	0.89[EUR][1000 genomes]
rs10210693	0.89[EUR][1000 genomes]
rs10210791	0.89[EUR][1000 genomes]
rs10210883	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1025240	0.89[EUR][1000 genomes]
rs1025241	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1035825	0.90[EUR][1000 genomes]
rs1035828	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1045327	0.85[ASN][1000 genomes]
rs10515934	0.91[ASN][1000 genomes]
rs10803853	0.85[ASN][1000 genomes]
rs10803854	0.91[ASN][1000 genomes]
rs10803855	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10930448	0.91[ASN][1000 genomes]
rs10930449	0.91[ASN][1000 genomes]
rs10930453	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10930455	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10930456	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10930457	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11674590	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11696064	0.80[EUR][1000 genomes]
rs11899305	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12053543	0.83[EUR][1000 genomes]
rs12471930	0.91[ASN][1000 genomes]
rs12477649	0.85[EUR][1000 genomes]
rs12612871	0.91[ASN][1000 genomes]
rs12614580	0.91[EUR][1000 genomes]
rs12618232	0.81[EUR][1000 genomes]
rs12624094	0.84[EUR][1000 genomes]
rs12988738	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12996518	0.91[ASN][1000 genomes]
rs12997252	0.88[ASN][1000 genomes]
rs12998296	0.88[ASN][1000 genomes]
rs13000898	0.83[ASN][1000 genomes]
rs13004273	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13010307	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13015226	0.85[ASN][1000 genomes]
rs13025198	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13026662	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13030784	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13034529	0.90[EUR][1000 genomes]
rs13035460	0.85[ASN][1000 genomes]
rs13036123	0.86[EUR][1000 genomes]
rs13395669	0.87[EUR][1000 genomes]
rs13401706	0.89[EUR][1000 genomes]
rs13402107	0.88[EUR][1000 genomes]
rs13403285	0.89[EUR][1000 genomes]
rs13410683	0.85[EUR][1000 genomes]
rs13411575	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13419444	0.90[EUR][1000 genomes]
rs13425247	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13427723	0.89[EUR][1000 genomes]
rs13428613	0.89[EUR][1000 genomes]
rs13430489	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13432813	0.89[EUR][1000 genomes]
rs1344237	0.89[EUR][1000 genomes]
rs1529378	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1529391	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16859066	0.91[ASN][1000 genomes]
rs16859142	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17281735	0.91[ASN][1000 genomes]
rs17283147	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1962841	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1978592	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1991370	0.88[ASN][1000 genomes]
rs2010114	0.83[EUR][1000 genomes]
rs2033160	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2052808	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2059724	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2081715	0.89[EUR][1000 genomes]
rs2114595	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2114596	0.88[EUR][1000 genomes]
rs2114738	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2195117	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2217154	0.89[EUR][1000 genomes]
rs2356423	0.86[EUR][1000 genomes]
rs2356593	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2356597	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2356599	0.87[EUR][1000 genomes]
rs2356608	0.89[EUR][1000 genomes]
rs2555922	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2557794	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2557799	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2676131	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2676151	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723233	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723241	0.88[ASN][1000 genomes]
rs34004615	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34017170	1.00[ASN][1000 genomes]
rs34342928	0.88[ASN][1000 genomes]
rs34518725	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34792013	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34911788	0.85[ASN][1000 genomes]
rs35123411	0.91[ASN][1000 genomes]
rs35173138	0.90[EUR][1000 genomes]
rs35279794	0.88[ASN][1000 genomes]
rs35312173	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35864840	1.00[ASN][1000 genomes]
rs35890547	0.91[ASN][1000 genomes]
rs35900609	0.88[ASN][1000 genomes]
rs35987434	0.85[ASN][1000 genomes]
rs35988467	0.87[EUR][1000 genomes]
rs36058634	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3731990	0.82[EUR][1000 genomes]
rs3731991	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755121	0.90[EUR][1000 genomes]
rs3755125	0.85[ASN][1000 genomes]
rs3770423	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770428	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770433	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770435	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770440	0.91[ASN][1000 genomes]
rs3770441	0.85[ASN][1000 genomes]
rs4544401	0.90[EUR][1000 genomes]
rs4564745	0.89[EUR][1000 genomes]
rs4667673	0.89[EUR][1000 genomes]
rs4668349	0.81[ASN][1000 genomes]
rs4668350	0.81[ASN][1000 genomes]
rs4668355	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4668368	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5028603	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55758155	0.89[EUR][1000 genomes]
rs55996750	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56114146	0.88[ASN][1000 genomes]
rs56402728	0.89[EUR][1000 genomes]
rs56405950	0.89[EUR][1000 genomes]
rs6433267	0.85[ASN][1000 genomes]
rs6433276	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6709077	1.00[ASN][1000 genomes]
rs6711287	0.84[EUR][1000 genomes]
rs6714164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6714300	0.91[ASN][1000 genomes]
rs6715332	0.94[EUR][1000 genomes]
rs6715386	0.85[ASN][1000 genomes]
rs6716127	0.88[EUR][1000 genomes]
rs6719647	0.88[ASN][1000 genomes]
rs6722537	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724493	0.85[ASN][1000 genomes]
rs6729847	0.85[ASN][1000 genomes]
rs6730417	0.88[EUR][1000 genomes]
rs6732229	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6733178	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6734542	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6734903	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742797	0.91[ASN][1000 genomes]
rs6742854	0.80[EUR][1000 genomes]
rs6743201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749427	0.87[EUR][1000 genomes]
rs6750849	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754315	0.90[EUR][1000 genomes]
rs6758331	0.88[ASN][1000 genomes]
rs6761596	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6761642	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71415229	0.85[ASN][1000 genomes]
rs71415232	0.91[ASN][1000 genomes]
rs71415235	0.88[ASN][1000 genomes]
rs731693	0.91[ASN][1000 genomes]
rs73976229	0.91[ASN][1000 genomes]
rs7421377	0.85[EUR][1000 genomes]
rs7570701	0.91[ASN][1000 genomes]
rs7578491	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7580629	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7581195	0.88[EUR][1000 genomes]
rs7581314	0.84[EUR][1000 genomes]
rs7585418	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7593193	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597940	0.82[EUR][1000 genomes]
rs7600914	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603316	0.89[EUR][1000 genomes]
rs7603340	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603460	0.90[EUR][1000 genomes]
rs7606502	0.90[EUR][1000 genomes]
rs7606822	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs930035	0.87[EUR][1000 genomes]
rs930036	0.87[EUR][1000 genomes]
rs958183	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs960222	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs964172	0.86[EUR][1000 genomes]
rs965518	0.88[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16859081	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

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	chr2:171831000-171850000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:171831200-171857400	Weak transcription	HSMMtube	muscle
5	chr2:171831400-171849400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:171831400-171857000	Weak transcription	NHEK	skin
7	chr2:171831400-171879200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:171831400-171916200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:171832600-171852200	Weak transcription	Fetal Intestine Small	intestine
10	chr2:171833000-171848800	Weak transcription	HepG2	liver
11	chr2:171837600-171849200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:171838400-171849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:171838600-171862000	Weak transcription	Ovary	ovary
14	chr2:171838800-171861800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:171839000-171852400	Weak transcription	NHLF	lung
16	chr2:171839200-171854800	Weak transcription	Pancreas	Pancrea
17	chr2:171840800-171861800	Weak transcription	Small Intestine	intestine
18	chr2:171840800-171879200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:171841000-171848800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:171841000-171852400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:171841000-171862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:171841000-171865400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:171841000-171877800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:171841000-171895800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:171841400-171849800	Weak transcription	Brain Substantia Nigra	brain
26	chr2:171841600-171859000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:171841600-171940000	Weak transcription	Right Ventricle	heart
28	chr2:171842200-171848200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:171842200-171849000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:171842200-171849400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:171842200-171892000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:171842400-171857600	Weak transcription	Fetal Brain Female	brain
33	chr2:171842600-171912000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:171842800-171852400	Weak transcription	Aorta	Aorta
35	chr2:171843000-171849200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:171843000-171877400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:171843200-171848400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:171843200-171850200	Weak transcription	Left Ventricle	heart
39	chr2:171843200-171863200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:171843200-171871800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:171843400-171848800	Weak transcription	Fetal Kidney	kidney
42	chr2:171843400-171852800	Weak transcription	Thymus	Thymus
43	chr2:171843600-171851200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:171843600-171852200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:171843600-171857000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:171843800-171863400	Strong transcription	Fetal Thymus	thymus
47	chr2:171844600-171853800	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:171844600-171868800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:171844800-171854200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:171844800-171863400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links