Variant report

Variant	rs16871972
Chromosome Location	chr5:41849255-41849256
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 185 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs10045473	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10051322	0.93[ASN][1000 genomes]
rs10059424	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10060170	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10062703	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10064298	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10064380	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10069638	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1006996	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10070201	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10075064	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10077481	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10472357	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10941557	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10941559	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1118104	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11738517	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11739106	1.00[EUR][1000 genomes]
rs11739257	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740524	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740946	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11742249	0.89[EUR][1000 genomes]
rs11744279	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744516	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11744623	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745373	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11746511	1.00[EUR][1000 genomes]
rs11747881	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11747921	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749008	0.96[EUR][1000 genomes]
rs11750607	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs11750760	0.93[CEU][hapmap];0.99[EUR][1000 genomes]
rs11750790	0.87[CEU][hapmap];0.99[EUR][1000 genomes]
rs1175227	0.93[ASN][1000 genomes]
rs13153468	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs13153837	1.00[EUR][1000 genomes]
rs13155013	0.85[EUR][1000 genomes]
rs13155338	0.84[EUR][1000 genomes]
rs13156367	0.89[EUR][1000 genomes]
rs13162040	0.99[EUR][1000 genomes]
rs13163137	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13164201	1.00[EUR][1000 genomes]
rs13165731	0.99[EUR][1000 genomes]
rs13167578	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs13168035	0.99[EUR][1000 genomes]
rs13169285	0.91[EUR][1000 genomes]
rs13169977	0.99[EUR][1000 genomes]
rs13170096	0.91[EUR][1000 genomes]
rs13176368	0.99[EUR][1000 genomes]
rs13177937	0.92[ASW][hapmap];0.89[CEU][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs13179852	0.99[EUR][1000 genomes]
rs13180405	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs13180475	0.85[EUR][1000 genomes]
rs13182336	0.99[EUR][1000 genomes]
rs13185973	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs13186086	0.84[EUR][1000 genomes]
rs13189403	0.94[EUR][1000 genomes]
rs13357951	0.93[ASN][1000 genomes]
rs13360001	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1345781	0.94[EUR][1000 genomes]
rs1355089	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1389756	0.85[EUR][1000 genomes]
rs1494392	0.86[ASN][1000 genomes]
rs1508815	0.99[EUR][1000 genomes]
rs1508816	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1508818	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs1533014	1.00[ASN][1000 genomes]
rs16871940	0.86[ASN][1000 genomes]
rs16871955	0.99[EUR][1000 genomes]
rs16900142	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17739462	1.00[ASN][1000 genomes]
rs17847285	1.00[ASN][1000 genomes]
rs1876653	0.99[EUR][1000 genomes]
rs1876654	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2081102	0.85[EUR][1000 genomes]
rs2113053	0.93[ASN][1000 genomes]
rs2231910	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2231917	0.93[ASN][1000 genomes]
rs2329815	1.00[ASN][1000 genomes]
rs277406	0.93[ASN][1000 genomes]
rs277407	0.93[ASN][1000 genomes]
rs277414	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs277416	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316760	0.86[ASN][1000 genomes]
rs33967331	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34048302	0.91[EUR][1000 genomes]
rs34071445	0.99[EUR][1000 genomes]
rs34193394	0.84[EUR][1000 genomes]
rs34329864	0.99[EUR][1000 genomes]
rs34339137	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34369972	0.99[EUR][1000 genomes]
rs34412181	0.96[EUR][1000 genomes]
rs34500930	0.99[EUR][1000 genomes]
rs34569700	0.99[EUR][1000 genomes]
rs34625465	0.99[EUR][1000 genomes]
rs34663371	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34841703	0.99[EUR][1000 genomes]
rs34873414	0.99[EUR][1000 genomes]
rs34898214	0.84[EUR][1000 genomes]
rs35077044	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154057	1.00[ASN][1000 genomes]
rs35244816	0.88[EUR][1000 genomes]
rs35252930	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35343042	0.97[EUR][1000 genomes]
rs35613904	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35691805	0.84[EUR][1000 genomes]
rs35748945	0.91[EUR][1000 genomes]
rs35764180	0.97[EUR][1000 genomes]
rs35861205	0.99[EUR][1000 genomes]
rs36005620	0.99[EUR][1000 genomes]
rs36009913	0.89[EUR][1000 genomes]
rs36113900	0.99[EUR][1000 genomes]
rs3926618	0.99[EUR][1000 genomes]
rs4050986	1.00[ASN][1000 genomes]
rs4245982	0.86[ASN][1000 genomes]
rs4289604	0.93[ASN][1000 genomes]
rs4324728	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4957171	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957173	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957174	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957175	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957176	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957177	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957178	0.93[ASN][1000 genomes]
rs4957180	0.93[ASN][1000 genomes]
rs4957419	0.86[ASN][1000 genomes]
rs4957422	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957423	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957424	1.00[ASN][1000 genomes]
rs4957428	1.00[ASN][1000 genomes]
rs4957429	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957430	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957431	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957432	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957433	0.93[ASN][1000 genomes]
rs4957434	1.00[JPT][hapmap]
rs4957435	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957436	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957437	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957438	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957439	0.93[ASN][1000 genomes]
rs55817686	0.97[EUR][1000 genomes]
rs56017638	0.99[EUR][1000 genomes]
rs60209308	0.99[EUR][1000 genomes]
rs62360521	0.84[EUR][1000 genomes]
rs62360542	0.92[EUR][1000 genomes]
rs626907	1.00[JPT][hapmap]
rs6451581	0.86[ASN][1000 genomes]
rs6451582	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs66820325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67114999	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67206815	0.97[EUR][1000 genomes]
rs676067	0.93[ASN][1000 genomes]
rs67715253	0.97[EUR][1000 genomes]
rs67869805	0.97[EUR][1000 genomes]
rs6865448	0.81[EUR][1000 genomes]
rs6866549	0.99[EUR][1000 genomes]
rs6879341	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs6881206	0.86[EUR][1000 genomes]
rs6881873	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883144	0.99[EUR][1000 genomes]
rs6888816	0.99[EUR][1000 genomes]
rs6889217	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72746918	0.97[EUR][1000 genomes]
rs72746919	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72746957	0.99[EUR][1000 genomes]
rs72746983	0.93[ASN][1000 genomes]
rs72746996	0.93[ASN][1000 genomes]
rs7709500	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7712911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721136	0.81[EUR][1000 genomes]
rs7724934	0.97[EUR][1000 genomes]
rs7725264	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs7728482	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7729014	1.00[ASN][1000 genomes]
rs7733096	1.00[ASN][1000 genomes]
rs9292825	0.93[ASN][1000 genomes]
rs951883	0.99[EUR][1000 genomes]
rs964267	0.99[EUR][1000 genomes]
rs9687619	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9763018	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830271	chr5:41716527-41895710	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv4811	chr5:41844522-41887353	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16871972	LIFR	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41818400-41852000	Weak transcription	Small Intestine	intestine
2	chr5:41819200-41852800	Weak transcription	Pancreas	Pancrea
3	chr5:41824600-41859400	Weak transcription	Spleen	Spleen
4	chr5:41827800-41849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:41829400-41851000	Weak transcription	Fetal Intestine Small	intestine
6	chr5:41830800-41849800	Weak transcription	Gastric	stomach
7	chr5:41831200-41854400	Weak transcription	Colonic Mucosa	Colon
8	chr5:41832800-41850000	Weak transcription	Esophagus	oesophagus
9	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:41836000-41857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:41836400-41849400	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:41836600-41849400	Weak transcription	HSMM	muscle
13	chr5:41836600-41863800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:41837000-41850000	Weak transcription	Brain Angular Gyrus	brain
15	chr5:41837200-41858600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:41839000-41851000	Weak transcription	Lung	lung
17	chr5:41839200-41849800	Weak transcription	Fetal Stomach	stomach
18	chr5:41839200-41850200	Weak transcription	Fetal Intestine Large	intestine
19	chr5:41839400-41849400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:41841600-41849800	Weak transcription	Aorta	Aorta
21	chr5:41841800-41849800	Weak transcription	Right Ventricle	heart
22	chr5:41841800-41869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:41843800-41855600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:41845400-41849800	Weak transcription	Left Ventricle	heart
25	chr5:41849000-41849800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:41849000-41849800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:41849000-41853000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:41849000-41853800	Strong transcription	NHDF-Ad	bronchial
29	chr5:41849000-41855200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:41849000-41856000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr5:41849000-41856200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:41849000-41856400	Strong transcription	Adipose Nuclei	Adipose
33	chr5:41849000-41856600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:41849000-41856600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:41849000-41857000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:41849000-41857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:41849000-41857200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:41849000-41857200	Strong transcription	K562	blood
39	chr5:41849000-41857800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:41849000-41862200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:41849000-41862600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:41849000-41862800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr5:41849000-41862800	Strong transcription	Fetal Thymus	thymus
44	chr5:41849200-41849400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:41849200-41849400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:41849200-41849400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr5:41849200-41849400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:41849200-41849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
49	chr5:41849200-41849800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:41849200-41849800	Strong transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links