Variant report

Variant	rs836794
Chromosome Location	chr5:80012251-80012252
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs13161245	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1346463	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs1346464	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs1382539	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1382540	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1382543	0.95[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1478834	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1620258	0.83[AMR][1000 genomes]
rs1628627	0.89[CEU][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs1643638	0.94[CEU][hapmap]
rs1643649	0.89[CEU][hapmap]
rs1643650	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1643657	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1643658	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1643659	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1650648	0.93[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs1650650	0.95[CEU][hapmap]
rs1650651	0.95[CEU][hapmap]
rs1650652	0.94[CEU][hapmap]
rs1650653	0.95[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1650654	0.95[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1650658	0.95[CEU][hapmap]
rs1650663	0.95[CEU][hapmap]
rs1650665	0.95[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1650666	0.95[CEU][hapmap]
rs1650667	0.95[CEU][hapmap]
rs1650670	0.95[CEU][hapmap]
rs1650692	0.89[CEU][hapmap]
rs1650709	0.89[CEU][hapmap]
rs1650737	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1650742	0.82[AMR][1000 genomes]
rs1650749	0.83[AMR][1000 genomes]
rs1650750	0.83[AMR][1000 genomes]
rs1677626	0.89[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs1677628	0.95[CEU][hapmap]
rs1677629	0.94[CEU][hapmap]
rs1677630	0.83[AMR][1000 genomes]
rs1677635	0.94[CEU][hapmap]
rs1677636	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1677638	0.94[CEU][hapmap]
rs1677639	0.94[CEU][hapmap]
rs1677641	0.94[CEU][hapmap]
rs1677643	0.95[CEU][hapmap]
rs1677650	0.95[CEU][hapmap]
rs1677652	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs1677653	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs1677654	0.83[AMR][1000 genomes]
rs1677655	0.83[AMR][1000 genomes]
rs1677691	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1677692	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1677693	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1677694	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1677703	0.95[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1677707	0.83[AMR][1000 genomes]
rs1677709	0.83[AMR][1000 genomes]
rs1824837	0.95[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1824838	0.95[CEU][hapmap]
rs1824839	0.95[CEU][hapmap]
rs245331	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs245332	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2560424	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs2560425	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2618369	0.83[AMR][1000 genomes]
rs2618372	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs26267	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs26282	0.87[EUR][1000 genomes]
rs28027	0.88[EUR][1000 genomes]
rs2897262	0.95[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs32959	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs366371	1.00[CHB][hapmap]
rs6151614	0.95[CEU][hapmap]
rs6151615	1.00[CEU][hapmap]
rs6151618	0.94[CEU][hapmap]
rs6151619	0.95[CEU][hapmap]
rs6151620	0.95[CEU][hapmap]
rs836795	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs836798	0.83[AMR][1000 genomes]
rs836799	0.83[AMR][1000 genomes]
rs836800	0.83[AMR][1000 genomes]
rs836801	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs836802	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs836804	0.81[AMR][1000 genomes]
rs836806	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs836808	0.93[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs836809	0.83[AMR][1000 genomes]
rs836810	0.83[AMR][1000 genomes]
rs836813	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs836816	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs836818	0.89[CEU][hapmap]
rs836821	0.89[CEU][hapmap]
rs836822	0.89[CEU][hapmap]
rs836823	0.89[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs844368	0.83[AMR][1000 genomes]
rs844369	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs844370	0.89[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs857016	0.83[AMR][1000 genomes]
rs861372	0.83[AMR][1000 genomes]
rs863214	0.93[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes]
rs863215	0.89[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs836794	DHFR	cis	Heart Left Ventricle	GTEx
rs836794	MSH3	cis	Whole Blood	GTEx
rs836794	RASGRF2	cis	cerebellum	SCAN
rs836794	MSH3	cis	Thyroid	GTEx
rs836794	DHFR	cis	Muscle Skeletal	GTEx
rs836794	MSH3	cis	cerebellum	SCAN
rs836794	MCART6	trans	cerebellum	SCAN
rs836794	MSH3	cis	parietal	SCAN
rs836794	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs836794	ANKRD34B	cis	Whole Blood	GTEx
rs836794	DHFR	cis	Adipose Subcutaneous	GTEx
rs836794	DHFR	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
2	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
3	chr5:79962800-80015600	Weak transcription	A549	lung
4	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
5	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:79965000-80021400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:79971600-80022200	Weak transcription	HMEC	breast
8	chr5:79971800-80015400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:79973200-80021600	Weak transcription	NH-A	brain
12	chr5:79974000-80021200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:79975200-80022800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:79975600-80015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:79975600-80022000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:79975800-80015600	Weak transcription	Brain Substantia Nigra	brain
17	chr5:79975800-80015800	Weak transcription	Fetal Brain Female	brain
18	chr5:79979200-80013800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:79979800-80015600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:79980000-80015800	Weak transcription	Fetal Kidney	kidney
21	chr5:79983400-80021600	Weak transcription	Brain Angular Gyrus	brain
22	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:79992400-80021000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:79994400-80016000	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:79998400-80021400	Weak transcription	K562	blood
26	chr5:79998400-80021600	Weak transcription	Spleen	Spleen
27	chr5:79998600-80015600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
29	chr5:79998800-80022200	Weak transcription	Gastric	stomach
30	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:79999800-80021200	Weak transcription	Placenta	Placenta
32	chr5:80000000-80015600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:80000000-80021200	Weak transcription	Osteobl	bone
34	chr5:80000200-80021400	Weak transcription	HSMMtube	muscle
35	chr5:80000200-80021600	Weak transcription	Colonic Mucosa	Colon
36	chr5:80000200-80038600	Weak transcription	Esophagus	oesophagus
37	chr5:80000400-80015600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:80000400-80036800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:80000400-80036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:80000600-80015600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:80000600-80015600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:80000600-80015600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:80001200-80015600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:80001600-80015400	Weak transcription	Fetal Lung	lung
45	chr5:80003600-80015600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:80003600-80021200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:80003600-80021800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:80003600-80030400	Weak transcription	NHLF	lung
49	chr5:80004000-80026400	Weak transcription	Fetal Heart	heart
50	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial

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