Variant report

Variant	rs1611823
Chromosome Location	chr1:76221706-76221707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1061337	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873685	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161437	0.90[EUR][1000 genomes]
rs11161468	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161493	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161510	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161511	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161515	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161521	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146574	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146580	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146581	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146588	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091720	0.91[EUR][1000 genomes]
rs12094842	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12123977	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126481	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126607	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127402	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	0.81[EUR][1000 genomes]
rs12136754	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250874	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251075	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1303169	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313071	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.90[EUR][1000 genomes]
rs1498315	0.88[EUR][1000 genomes]
rs1498316	0.83[EUR][1000 genomes]
rs1498317	0.93[EUR][1000 genomes]
rs1612097	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613437	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1694419	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694424	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587071	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767455	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767456	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767458	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770511	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855136	0.84[EUR][1000 genomes]
rs1858536	0.94[EUR][1000 genomes]
rs1890451	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890452	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066183	0.92[EUR][1000 genomes]
rs2153126	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173378	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185152	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185435	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185436	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.81[EUR][1000 genomes]
rs2275378	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788654	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28602663	0.85[EUR][1000 genomes]
rs3818855	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559448	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646961	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949674	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.88[EUR][1000 genomes]
rs4949875	0.85[EUR][1000 genomes]
rs4949876	0.89[EUR][1000 genomes]
rs4949877	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.85[EUR][1000 genomes]
rs57186386	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61289992	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61622554	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797339	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797340	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61799967	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799969	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61799988	0.80[EUR][1000 genomes]
rs61799990	0.81[EUR][1000 genomes]
rs6593514	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593515	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593585	0.82[EUR][1000 genomes]
rs6688749	0.85[EUR][1000 genomes]
rs72686191	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7513363	0.88[EUR][1000 genomes]
rs7513559	0.87[EUR][1000 genomes]
rs7515955	0.82[EUR][1000 genomes]
rs7516122	0.81[EUR][1000 genomes]
rs7516226	0.85[EUR][1000 genomes]
rs7518038	0.87[EUR][1000 genomes]
rs7524467	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533888	0.87[EUR][1000 genomes]
rs7534754	0.91[EUR][1000 genomes]
rs7535991	0.94[EUR][1000 genomes]
rs7539246	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541058	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544117	0.94[EUR][1000 genomes]
rs7546641	0.93[EUR][1000 genomes]
rs7548962	0.82[EUR][1000 genomes]
rs7549167	0.82[EUR][1000 genomes]
rs7550974	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.82[EUR][1000 genomes]
rs7554984	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8763	0.93[ASN][1000 genomes]
rs942270	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9662166	0.85[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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1611823	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:76196000-76222000	Strong transcription	Liver	Liver
4	chr1:76202000-76225000	Weak transcription	Stomach Mucosa	stomach
5	chr1:76203400-76230800	Weak transcription	NHDF-Ad	bronchial
6	chr1:76204800-76229000	Weak transcription	Psoas Muscle	Psoas
7	chr1:76208600-76223800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:76208800-76231400	Weak transcription	A549	lung
9	chr1:76208800-76231400	Weak transcription	NHEK	skin
10	chr1:76208800-76231600	Weak transcription	Hela-S3	cervix
11	chr1:76209000-76230800	Weak transcription	HUVEC	blood vessel
12	chr1:76209000-76230800	Weak transcription	NHLF	lung
13	chr1:76210200-76223000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:76210200-76231800	Weak transcription	HSMMtube	muscle
15	chr1:76211600-76230800	Weak transcription	HMEC	breast
16	chr1:76214200-76221800	Strong transcription	Adipose Nuclei	Adipose
17	chr1:76215000-76221800	Strong transcription	Primary T cells from cord blood	blood
18	chr1:76215600-76221800	Strong transcription	Dnd41	blood
19	chr1:76215800-76221800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:76215800-76222000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:76215800-76222000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:76216000-76221800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:76216000-76221800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:76216000-76221800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:76216000-76222000	Strong transcription	Left Ventricle	heart
26	chr1:76216000-76222200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:76216000-76222400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:76216200-76222000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:76217000-76222000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:76217600-76231400	Weak transcription	Osteobl	bone
31	chr1:76217800-76222000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:76218000-76222600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:76219200-76221800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
34	chr1:76219400-76222000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:76219400-76222000	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr1:76219600-76222000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
37	chr1:76219600-76222000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr1:76219600-76222000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr1:76219600-76222000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:76219600-76222000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
41	chr1:76219600-76222000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
42	chr1:76219600-76222000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr1:76219600-76222600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:76219600-76230600	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:76219800-76221800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:76219800-76222000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:76219800-76222000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:76219800-76222200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr1:76220000-76222000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:76220000-76222000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links