Variant report

Variant	rs3732182
Chromosome Location	chr2:47693706-47693707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10175959	0.93[ASN][1000 genomes]
rs10175972	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10179452	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10185866	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs10188090	0.93[ASN][1000 genomes]
rs10206575	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10206782	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10209369	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs10495945	0.80[CHB][hapmap]
rs11684661	0.93[ASN][1000 genomes]
rs11684737	0.93[ASN][1000 genomes]
rs11694689	0.89[ASN][1000 genomes]
rs11886591	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12712993	0.82[ASN][1000 genomes]
rs12712994	0.82[ASN][1000 genomes]
rs12991125	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13031342	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1981927	0.80[ASN][1000 genomes]
rs1981928	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2059520	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs2162121	0.87[ASN][1000 genomes]
rs2347795	0.82[ASN][1000 genomes]
rs3732183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764959	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764960	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771274	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs3771275	0.82[ASN][1000 genomes]
rs3771276	0.85[ASN][1000 genomes]
rs3771278	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771279	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771280	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771281	0.96[ASN][1000 genomes]
rs3821227	0.94[ASN][1000 genomes]
rs4550716	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs4583514	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4596025	0.82[ASN][1000 genomes]
rs6544989	0.82[ASN][1000 genomes]
rs6544990	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6544992	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6711675	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6720549	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6724382	0.85[ASN][1000 genomes]
rs6724876	0.85[ASN][1000 genomes]
rs6725042	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6726691	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726832	0.80[ASN][1000 genomes]
rs6729015	0.86[ASN][1000 genomes]
rs6737303	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6748435	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6754473	0.96[ASN][1000 genomes]
rs6757035	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6758327	0.87[ASN][1000 genomes]
rs6759990	0.81[CHB][hapmap]
rs7565513	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7584256	0.87[CEU][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs7585174	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586575	0.89[ASN][1000 genomes]
rs7588420	0.88[EUR][1000 genomes]
rs7596629	0.98[ASN][1000 genomes]
rs7599880	0.81[ASN][1000 genomes]
rs7607076	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs876936	0.85[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv527823	chr2:47645249-47709704	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3732182	MSH2	cis	Artery Tibial	GTEx
rs3732182	MSH2	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47631400-47697000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:47631400-47714400	Weak transcription	Right Ventricle	heart
3	chr2:47631800-47696600	Weak transcription	Esophagus	oesophagus
4	chr2:47631800-47700000	Weak transcription	Colonic Mucosa	Colon
5	chr2:47631800-47704200	Weak transcription	Psoas Muscle	Psoas
6	chr2:47633000-47714000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:47643600-47703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:47658000-47707000	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:47658000-47714200	Weak transcription	Small Intestine	intestine
10	chr2:47658200-47709200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:47658200-47710400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:47658200-47713400	Weak transcription	Fetal Heart	heart
13	chr2:47658200-47714200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:47658200-47714800	Weak transcription	HSMMtube	muscle
15	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:47658400-47695200	Weak transcription	NHLF	lung
17	chr2:47658400-47713600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:47658400-47716000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:47658800-47712600	Weak transcription	Osteobl	bone
20	chr2:47673800-47712400	Weak transcription	NHDF-Ad	bronchial
21	chr2:47674800-47696200	Weak transcription	Lung	lung
22	chr2:47677000-47710800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:47679800-47712600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:47680000-47700000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:47685000-47715000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:47685400-47701200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:47686400-47712600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:47686400-47712600	Strong transcription	Dnd41	blood
29	chr2:47687200-47706800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:47688200-47698200	Weak transcription	HUVEC	blood vessel
31	chr2:47688600-47703000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:47689200-47713000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:47689400-47694400	Strong transcription	HepG2	liver
34	chr2:47689400-47700800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:47689400-47703000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:47689400-47712800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:47689800-47694200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:47689800-47700200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:47689800-47713000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr2:47690000-47694200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:47690000-47694200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:47690000-47694400	Strong transcription	Primary T cells from cord blood	blood
43	chr2:47690000-47694400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:47690000-47706800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:47690200-47694200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:47690200-47694200	Strong transcription	Fetal Lung	lung
47	chr2:47690200-47694200	Strong transcription	A549	lung
48	chr2:47690200-47695400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:47690200-47700400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:47690200-47700800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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