Variant report

Variant	rs1146588
Chromosome Location	chr1:76229787-76229788
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76225609..76234140-chr1:76249320..76256385,15	K562	blood:
2	chr1:76226797..76230209-chr1:76256987..76259479,3	K562	blood:
3	chr1:76225579..76234839-chr1:76250485..76256385,12	K562	blood:
4	chr1:76189779..76193435-chr1:76229737..76232893,5	K562	blood:
5	chr1:76227948..76230209-chr1:76256987..76259479,2	K562	blood:
6	chr1:76222580..76224915-chr1:76228068..76230372,2	K562	blood:

Variant related genes	Relation type
ENSG00000207241	Chromatin interaction
ENSG00000201487	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1061337	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873685	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161437	0.89[EUR][1000 genomes]
rs11161468	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161510	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161511	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161515	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161521	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146580	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146581	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146646	0.81[EUR][1000 genomes]
rs12091720	0.91[EUR][1000 genomes]
rs12094842	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12123977	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126481	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126607	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127402	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs12136754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250874	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251075	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251078	0.96[CEU][hapmap]
rs1251079	0.96[CEU][hapmap]
rs1303169	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313071	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.90[EUR][1000 genomes]
rs1498315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs1498316	0.83[EUR][1000 genomes]
rs1498317	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1611823	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613437	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1694419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694424	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587071	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767455	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767456	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767458	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770511	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855136	0.84[EUR][1000 genomes]
rs1858536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs1890451	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890452	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs2153126	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185152	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185435	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185436	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.82[EUR][1000 genomes]
rs2275378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788654	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28602663	0.87[EUR][1000 genomes]
rs3818855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559448	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646961	0.92[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949674	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs4949875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs4949876	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4949877	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.87[EUR][1000 genomes]
rs57186386	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61289992	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61622554	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797339	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797340	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61799967	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799969	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61799988	0.82[EUR][1000 genomes]
rs61799990	0.83[EUR][1000 genomes]
rs6593514	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593515	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593585	0.81[EUR][1000 genomes]
rs6688749	0.84[EUR][1000 genomes]
rs72686191	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7513363	0.88[EUR][1000 genomes]
rs7513559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7515955	0.81[EUR][1000 genomes]
rs7516122	0.81[EUR][1000 genomes]
rs7516226	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7518038	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7524467	0.96[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs7534754	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7535991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs7539246	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541058	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs7546641	0.93[EUR][1000 genomes]
rs7548962	0.81[EUR][1000 genomes]
rs7549167	0.81[EUR][1000 genomes]
rs7550974	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.81[EUR][1000 genomes]
rs7554984	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8763	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs942270	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9662166	0.87[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
rs1146588	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76203400-76230800	Weak transcription	NHDF-Ad	bronchial
2	chr1:76208800-76231400	Weak transcription	A549	lung
3	chr1:76208800-76231400	Weak transcription	NHEK	skin
4	chr1:76208800-76231600	Weak transcription	Hela-S3	cervix
5	chr1:76209000-76230800	Weak transcription	HUVEC	blood vessel
6	chr1:76209000-76230800	Weak transcription	NHLF	lung
7	chr1:76210200-76231800	Weak transcription	HSMMtube	muscle
8	chr1:76211600-76230800	Weak transcription	HMEC	breast
9	chr1:76217600-76231400	Weak transcription	Osteobl	bone
10	chr1:76219600-76230600	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:76221200-76229800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:76221200-76230200	Weak transcription	Small Intestine	intestine
13	chr1:76221200-76231400	Weak transcription	Gastric	stomach
14	chr1:76221200-76238400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:76221400-76230000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:76221400-76230600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:76221400-76230600	Weak transcription	Colonic Mucosa	Colon
18	chr1:76221400-76231200	Weak transcription	NH-A	brain
19	chr1:76221400-76231400	Weak transcription	Pancreas	Pancrea
20	chr1:76221400-76233200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:76221600-76230800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:76221600-76230800	Weak transcription	Lung	lung
23	chr1:76221600-76231000	Weak transcription	Aorta	Aorta
24	chr1:76221600-76231000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:76221600-76231000	Weak transcription	Right Ventricle	heart
26	chr1:76221600-76231200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:76221600-76231400	Weak transcription	Fetal Heart	heart
28	chr1:76221600-76231400	Weak transcription	Ovary	ovary
29	chr1:76221600-76231400	Weak transcription	HSMM	muscle
30	chr1:76221600-76231600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:76221600-76231600	Weak transcription	Esophagus	oesophagus
32	chr1:76221600-76231800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:76221600-76232200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:76221600-76234200	Weak transcription	Thymus	Thymus
35	chr1:76221800-76230000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:76221800-76231400	Weak transcription	Primary T cells from cord blood	blood
37	chr1:76221800-76232600	Weak transcription	Fetal Brain Male	brain
38	chr1:76222000-76230000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:76222000-76230800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:76222000-76231000	Weak transcription	Fetal Lung	lung
41	chr1:76222000-76231200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:76222000-76231600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:76222000-76231600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:76222000-76231600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:76222000-76233400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:76222000-76233800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:76222000-76236600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:76222000-76237000	Weak transcription	Brain Angular Gyrus	brain
49	chr1:76222200-76231600	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:76223800-76236600	Weak transcription	H1 Cell Line	embryonic stem cell

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