Variant report

Variant	rs32952
Chromosome Location	chr5:80021445-80021446
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10044730	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743909	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245335	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32950	0.81[EUR][1000 genomes]
rs33008	0.81[CHD][hapmap]
rs3776967	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776968	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151627	0.86[CHD][hapmap]
rs6151653	0.86[CHD][hapmap]
rs6151704	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709909	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712332	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs32952	MSH3	cis	lymphoblastoid	seeQTL
rs32952	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs32952	DHFR	cis	Muscle Skeletal	GTEx
rs32952	DHFR///LOC643509	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	chr5:79971600-80022200	Weak transcription	HMEC	breast
4	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:79973200-80021600	Weak transcription	NH-A	brain
7	chr5:79975200-80022800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:79975600-80022000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:79983400-80021600	Weak transcription	Brain Angular Gyrus	brain
10	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
11	chr5:79998400-80021600	Weak transcription	Spleen	Spleen
12	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
13	chr5:79998800-80022200	Weak transcription	Gastric	stomach
14	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:80000200-80021600	Weak transcription	Colonic Mucosa	Colon
16	chr5:80000200-80038600	Weak transcription	Esophagus	oesophagus
17	chr5:80000400-80036800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:80000400-80036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:80003600-80021800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:80003600-80030400	Weak transcription	NHLF	lung
21	chr5:80004000-80026400	Weak transcription	Fetal Heart	heart
22	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
23	chr5:80006600-80021600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:80007400-80022000	Weak transcription	Lung	lung
25	chr5:80007600-80023600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:80008000-80021600	Weak transcription	Thymus	Thymus
27	chr5:80009000-80021600	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:80009600-80024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:80009800-80022600	Weak transcription	HUVEC	blood vessel
30	chr5:80009800-80024000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:80009800-80039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:80010600-80036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:80010800-80032400	Weak transcription	Stomach Mucosa	stomach
34	chr5:80015800-80032400	Weak transcription	Pancreas	Pancrea
35	chr5:80016000-80021600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:80016000-80021600	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:80016000-80021600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:80016000-80021600	Weak transcription	NHEK	skin
39	chr5:80016000-80021800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:80016000-80021800	Weak transcription	Fetal Brain Female	brain
41	chr5:80016000-80022600	Weak transcription	Aorta	Aorta
42	chr5:80016000-80038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:80016000-80040600	Weak transcription	Small Intestine	intestine
44	chr5:80016200-80021600	Weak transcription	Fetal Thymus	thymus
45	chr5:80016200-80040600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr5:80016200-80040600	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr5:80016400-80021600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:80016400-80021600	Weak transcription	A549	lung
50	chr5:80016400-80022200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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