Variant report

Variant	rs245015
Chromosome Location	chr5:80022307-80022308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12517451	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1621852	0.80[EUR][1000 genomes]
rs1650647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1650649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1650697	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1650748	0.80[EUR][1000 genomes]
rs1650751	0.80[EUR][1000 genomes]
rs173437	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2035256	0.82[ASN][1000 genomes]
rs245010	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs245013	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs245016	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26784	0.87[ASN][1000 genomes]
rs32950	0.85[ASN][1000 genomes]
rs368406	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3958547	0.82[ASN][1000 genomes]
rs40139	0.83[ASN][1000 genomes]
rs403236	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151766	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs836796	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836797	0.81[ASN][1000 genomes]
rs836805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs836814	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836815	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836817	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs863221	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs865644	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs245015	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs245015	MSH3	cis	Whole Blood	GTEx
rs245015	MSH3	cis	Heart Left Ventricle	GTEx

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	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:79975200-80022800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
7	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
8	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:80000200-80038600	Weak transcription	Esophagus	oesophagus
10	chr5:80000400-80036800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr5:80000400-80036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:80003600-80030400	Weak transcription	NHLF	lung
13	chr5:80004000-80026400	Weak transcription	Fetal Heart	heart
14	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
15	chr5:80007600-80023600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:80009600-80024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:80009800-80022600	Weak transcription	HUVEC	blood vessel
18	chr5:80009800-80024000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:80009800-80039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:80010600-80036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:80010800-80032400	Weak transcription	Stomach Mucosa	stomach
22	chr5:80015800-80032400	Weak transcription	Pancreas	Pancrea
23	chr5:80016000-80022600	Weak transcription	Aorta	Aorta
24	chr5:80016000-80038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:80016000-80040600	Weak transcription	Small Intestine	intestine
26	chr5:80016200-80040600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:80016200-80040600	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:80016400-80027800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:80016400-80032400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:80016400-80034200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:80016400-80038200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
34	chr5:80016600-80034200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:80020200-80043600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:80020400-80024400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:80020800-80030800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr5:80021000-80023000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:80021000-80026200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:80021200-80022400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr5:80021200-80023000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:80021200-80024200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr5:80021200-80024200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:80021200-80024200	Strong transcription	Fetal Kidney	kidney
45	chr5:80021200-80024600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:80021200-80024600	Strong transcription	Dnd41	blood
47	chr5:80021200-80025800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:80021200-80025800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:80021200-80026000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:80021200-80026000	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links