Variant report

Variant	rs2194664
Chromosome Location	chr2:67079443-67079444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10170124	0.86[AFR][1000 genomes]
rs10196555	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1073280	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109351	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1110585	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1111235	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713576	0.88[YRI][hapmap]
rs12713578	0.86[AFR][1000 genomes]
rs12713581	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12713582	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713583	0.93[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs13008648	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13018976	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13031245	0.90[ASN][1000 genomes]
rs13420432	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2161975	0.97[AFR][1000 genomes]
rs2194662	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2194663	0.94[AFR][1000 genomes]
rs2194665	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194667	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2216924	0.97[AFR][1000 genomes]
rs2216925	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671751	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671754	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728659	0.95[AFR][1000 genomes]
rs6728760	0.80[AFR][1000 genomes]
rs7599395	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601449	0.97[AFR][1000 genomes]
rs9798168	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009027	chr2:66947462-67114455	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv874246	chr2:67001969-67147854	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2194664	MDH1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67068400-67080200	Weak transcription	Ovary	ovary
2	chr2:67069000-67081400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:67074600-67080000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:67074600-67080000	Weak transcription	Fetal Kidney	kidney
5	chr2:67076200-67079600	Enhancers	Fetal Stomach	stomach
6	chr2:67076200-67081800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:67076200-67082400	Enhancers	Colon Smooth Muscle	Colon
8	chr2:67076200-67082400	Enhancers	NHLF	lung
9	chr2:67077200-67080800	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:67077600-67080000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:67077800-67079600	Enhancers	NHDF-Ad	bronchial
12	chr2:67077800-67080200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:67077800-67080600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:67078000-67079600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:67078000-67079600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:67078400-67081200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:67078600-67079600	Enhancers	HSMM	muscle
18	chr2:67078800-67080600	Weak transcription	HSMMtube	muscle
19	chr2:67079200-67080200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:67079200-67080200	Weak transcription	Pancreas	Pancrea
21	chr2:67079200-67080200	Weak transcription	NH-A	brain
22	chr2:67079200-67080600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:67079200-67080800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:67079200-67080800	Weak transcription	Osteobl	bone
25	chr2:67079200-67081000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:67079400-67079800	Weak transcription	Fetal Lung	lung

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