Variant report

Variant	rs2142860
Chromosome Location	chr1:209934753-209934754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10082248	1.00[CEU][hapmap]
rs10489343	1.00[AFR][1000 genomes]
rs10779514	1.00[AFR][1000 genomes]
rs10779515	1.00[AFR][1000 genomes]
rs10863789	1.00[AFR][1000 genomes]
rs10863790	1.00[AFR][1000 genomes]
rs1109430	1.00[AFR][1000 genomes]
rs11119345	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11119347	1.00[AFR][1000 genomes]
rs11119348	1.00[AFR][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12058100	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes]
rs12081405	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12405750	1.00[AFR][1000 genomes]
rs12561766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015076	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17015078	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17015217	0.84[AMR][1000 genomes]
rs17015255	1.00[AFR][1000 genomes]
rs17015268	1.00[AFR][1000 genomes]
rs17388240	1.00[AFR][1000 genomes]
rs1856161	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2038053	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2076149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076151	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2235370	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2235371	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2235377	1.00[AFR][1000 genomes]
rs2236902	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2272866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282740	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298930	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753517	1.00[AFR][1000 genomes]
rs41274836	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4545339	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844488	0.83[AMR][1000 genomes]
rs4844491	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844494	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4844496	1.00[AFR][1000 genomes]
rs4844893	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs56822893	0.85[EUR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58788672	0.83[EUR][1000 genomes]
rs6540547	1.00[CEU][hapmap]
rs6694238	1.00[CEU][hapmap]
rs7515014	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517461	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7528642	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7532021	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs846908	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
3	chr1:209930200-209935000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
4	chr1:209930800-209938800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:209931000-209941800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:209931000-209942000	Weak transcription	Esophagus	oesophagus
7	chr1:209931000-209943200	Weak transcription	Lung	lung
8	chr1:209931000-209943600	Weak transcription	Gastric	stomach
9	chr1:209931800-209935400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
10	chr1:209931800-209935800	Genic enhancers	Primary B cells from peripheral blood	blood
11	chr1:209931800-209940600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:209932000-209935200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
13	chr1:209932000-209936800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:209932200-209934800	Genic enhancers	GM12878-XiMat	blood
15	chr1:209932200-209935400	Genic enhancers	Fetal Thymus	thymus
16	chr1:209932200-209941200	Genic enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:209932200-209941400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:209932200-209941800	Weak transcription	Colonic Mucosa	Colon
19	chr1:209932200-209942000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:209932600-209934800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:209932600-209935400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
22	chr1:209932600-209936000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:209932600-209937800	Strong transcription	Dnd41	blood
24	chr1:209932600-209940000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:209932800-209935200	Genic enhancers	Primary B cells from cord blood	blood
26	chr1:209932800-209938000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:209932800-209939400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:209933000-209937800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:209933000-209940000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:209933000-209940800	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr1:209933200-209936200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:209933200-209939400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:209933200-209939400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:209933400-209935600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:209933400-209939400	Strong transcription	Thymus	Thymus
36	chr1:209933400-209940600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:209933600-209937800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:209933600-209940800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr1:209933800-209935400	Weak transcription	Spleen	Spleen
40	chr1:209933800-209938000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:209933800-209939200	Weak transcription	Fetal Intestine Small	intestine
42	chr1:209933800-209941600	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:209934000-209941600	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:209934200-209935200	Genic enhancers	Primary hematopoietic stem cells	blood
45	chr1:209934400-209934800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:209934400-209934800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:209934400-209934800	Enhancers	Osteobl	bone
48	chr1:209934400-209935000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:209934400-209935000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:209934400-209937800	Genic enhancers	Monocytes-CD14+_RO01746	blood

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