Variant report

Variant	rs245016
Chromosome Location	chr5:80021193-80021194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12517451	0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs1621852	0.84[EUR][1000 genomes]
rs1650647	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs1650649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1650697	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs1650748	0.84[EUR][1000 genomes]
rs1650751	0.84[EUR][1000 genomes]
rs1677646	0.81[EUR][1000 genomes]
rs173437	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2035256	0.86[ASN][1000 genomes]
rs245010	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245013	0.80[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs245015	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26779	0.85[AFR][1000 genomes]
rs26784	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs32950	0.89[ASN][1000 genomes]
rs368406	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3958547	0.86[ASN][1000 genomes]
rs40139	0.88[ASN][1000 genomes]
rs403236	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs425463	0.80[CHD][hapmap]
rs6151766	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs836796	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836797	0.83[ASN][1000 genomes]
rs836805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs836814	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836815	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836817	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs863221	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs865644	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs245016	MSH3	cis	lymphoblastoid	seeQTL
rs245016	MSH3	cis	parietal	SCAN
rs245016	MSH3	cis	cerebellum	SCAN
rs245016	JMY	cis	parietal	SCAN
rs245016	MSH3	cis	Heart Left Ventricle	GTEx
rs245016	MSH3	cis	Whole Blood	GTEx
rs245016	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
2	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:79965000-80021400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:79971600-80022200	Weak transcription	HMEC	breast
5	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:79973200-80021600	Weak transcription	NH-A	brain
8	chr5:79974000-80021200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:79975200-80022800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:79975600-80022000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:79983400-80021600	Weak transcription	Brain Angular Gyrus	brain
12	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
13	chr5:79998400-80021400	Weak transcription	K562	blood
14	chr5:79998400-80021600	Weak transcription	Spleen	Spleen
15	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
16	chr5:79998800-80022200	Weak transcription	Gastric	stomach
17	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:79999800-80021200	Weak transcription	Placenta	Placenta
19	chr5:80000000-80021200	Weak transcription	Osteobl	bone
20	chr5:80000200-80021400	Weak transcription	HSMMtube	muscle
21	chr5:80000200-80021600	Weak transcription	Colonic Mucosa	Colon
22	chr5:80000200-80038600	Weak transcription	Esophagus	oesophagus
23	chr5:80000400-80036800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:80000400-80036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:80003600-80021200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:80003600-80021800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:80003600-80030400	Weak transcription	NHLF	lung
28	chr5:80004000-80026400	Weak transcription	Fetal Heart	heart
29	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
30	chr5:80006600-80021600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:80007000-80021400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:80007400-80022000	Weak transcription	Lung	lung
33	chr5:80007600-80023600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:80007800-80021400	Weak transcription	Ovary	ovary
35	chr5:80008000-80021600	Weak transcription	Thymus	Thymus
36	chr5:80009000-80021600	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:80009400-80021400	Weak transcription	Brain Anterior Caudate	brain
38	chr5:80009600-80024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:80009800-80022600	Weak transcription	HUVEC	blood vessel
40	chr5:80009800-80024000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:80009800-80039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:80010200-80021400	Weak transcription	Left Ventricle	heart
43	chr5:80010600-80036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:80010800-80032400	Weak transcription	Stomach Mucosa	stomach
45	chr5:80011200-80021400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:80011200-80021400	Weak transcription	Hela-S3	cervix
47	chr5:80011800-80021200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:80012800-80021200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:80015800-80032400	Weak transcription	Pancreas	Pancrea
50	chr5:80016000-80021200	Weak transcription	Primary hematopoietic stem cells	blood

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