Variant report

Variant	rs12991487
Chromosome Location	chr2:10065523-10065524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10053405..10055914-chr2:10061703..10065567,3	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10495576	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1054561	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1054565	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10803706	0.80[EUR][1000 genomes]
rs10803707	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10803708	0.94[ASN][1000 genomes]
rs10803709	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10803710	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10929620	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10929621	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11677649	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12185678	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12185679	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12185707	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12464092	0.81[ASN][1000 genomes]
rs12465661	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467598	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12468764	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12471962	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12473944	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12479251	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12614753	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12615461	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12617033	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12621371	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12623211	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12623217	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12624026	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12991584	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12995394	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13000106	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13008907	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13025784	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1367385	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867226	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867233	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16867239	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867240	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1820965	0.96[AMR][1000 genomes]
rs1820966	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1820967	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1835426	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241665	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2303921	0.83[ASN][1000 genomes]
rs2357390	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2357391	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2884175	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34577787	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35609983	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36009173	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs372222	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3815977	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs392617	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs394308	0.81[ASN][1000 genomes]
rs409920	0.91[AMR][1000 genomes]
rs417271	0.81[ASN][1000 genomes]
rs445742	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs450085	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs450192	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668650	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668653	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4668654	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669487	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4669489	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4669490	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4669491	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4669492	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4669493	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4669497	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669500	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514905	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55664551	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56241824	0.85[AFR][1000 genomes]
rs564933	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs565683	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58979565	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62127468	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6707887	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742427	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9750736	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1006533	chr2:10030964-10065624	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004743	chr2:10031389-10065624	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1005938	chr2:10043181-10074384	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
3	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
5	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:10036000-10065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
15	chr2:10046000-10075200	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
17	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain
18	chr2:10049400-10077200	Weak transcription	Brain Angular Gyrus	brain
19	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:10052800-10076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:10053200-10077800	Weak transcription	Liver	Liver
23	chr2:10054600-10073400	Weak transcription	Brain Substantia Nigra	brain
24	chr2:10054800-10066000	Weak transcription	Fetal Brain Male	brain
25	chr2:10054800-10069200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:10054800-10072200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:10054800-10079000	Weak transcription	Fetal Kidney	kidney
28	chr2:10055000-10067600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:10055000-10072600	Weak transcription	Spleen	Spleen
30	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
31	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:10055200-10072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:10055200-10072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:10055200-10073200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:10055200-10079600	Weak transcription	K562	blood
37	chr2:10055200-10080800	Weak transcription	HMEC	breast
38	chr2:10055600-10073000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:10055800-10075800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:10056800-10074200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:10058800-10076000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
43	chr2:10059200-10068000	Weak transcription	Psoas Muscle	Psoas
44	chr2:10059200-10072800	Weak transcription	Left Ventricle	heart
45	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
46	chr2:10059600-10072600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:10060000-10073400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:10060200-10071200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:10060400-10073000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:10060400-10075800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links