Variant report

Variant	rs12713469
Chromosome Location	chr2:63059927-63059928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11682530	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs11688816	0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[ASN][1000 genomes]
rs12989754	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs13013218	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs13410889	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1420018	0.85[CHB][hapmap]
rs1553832	0.85[CHB][hapmap]
rs189671	0.85[CHB][hapmap]
rs2058566	0.85[CHB][hapmap];0.94[CHD][hapmap]
rs2136737	0.85[CHB][hapmap]
rs2215870	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs2430388	0.95[CHB][hapmap];0.94[CHD][hapmap]
rs2539978	0.89[ASW][hapmap];0.90[LWK][hapmap]
rs2539980	0.84[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[LWK][hapmap]
rs2539981	0.92[ASN][1000 genomes]
rs2539984	0.87[AFR][1000 genomes]
rs2539987	0.91[CHD][hapmap]
rs2710638	0.80[CHB][hapmap];0.94[CHD][hapmap]
rs2710641	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2710642	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs2710647	0.83[ASW][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs360797	0.80[CHD][hapmap]
rs360799	0.85[CHB][hapmap]
rs360800	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs360801	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs360804	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs360807	0.80[CHB][hapmap];0.91[CHD][hapmap]
rs360808	0.84[CEU][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs4461246	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs4671448	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545971	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs6714241	0.98[LWK][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes]
rs7562734	0.83[ASN][1000 genomes]
rs7573756	0.97[CHD][hapmap]
rs7591708	0.89[ASW][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.89[TSI][hapmap];0.93[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	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12713469	MDH1	cis	cerebellum	SCAN
rs12713469	WDPCP	cis	lymphoblastoid	seeQTL
rs12713469	COMMD1	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
2	chr2:63028600-63063400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:63031000-63083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:63031400-63082000	Weak transcription	Thymus	Thymus
5	chr2:63033800-63060600	Weak transcription	Aorta	Aorta
6	chr2:63040600-63082000	Weak transcription	Lung	lung
7	chr2:63041600-63060400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:63041800-63060400	Weak transcription	K562	blood
9	chr2:63044000-63060200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:63045400-63060200	Weak transcription	Psoas Muscle	Psoas
11	chr2:63045600-63072400	Weak transcription	NHEK	skin
12	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
13	chr2:63048800-63063400	Weak transcription	Right Ventricle	heart
14	chr2:63049600-63065800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:63050200-63060400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:63050800-63060400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:63051200-63060400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:63052200-63060000	Weak transcription	Small Intestine	intestine
21	chr2:63052200-63064400	Weak transcription	Placenta	Placenta
22	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
23	chr2:63052400-63062600	Weak transcription	Fetal Thymus	thymus
24	chr2:63052400-63062600	Strong transcription	HepG2	liver
25	chr2:63052600-63060400	Weak transcription	Fetal Brain Male	brain
26	chr2:63053200-63060200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:63053200-63060400	Strong transcription	Liver	Liver
28	chr2:63053200-63063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:63053400-63060400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:63053400-63060600	Strong transcription	NHDF-Ad	bronchial
31	chr2:63054000-63060000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:63054400-63060000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr2:63054400-63060200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:63054400-63060400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:63054400-63062200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:63054400-63063000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:63054600-63060200	Weak transcription	Primary B cells from cord blood	blood
38	chr2:63054600-63060200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:63054600-63060200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:63054600-63060200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:63054600-63060800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:63054600-63061800	Weak transcription	HSMMtube	muscle
43	chr2:63054600-63062200	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:63054600-63067800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:63054800-63060200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:63054800-63060200	Weak transcription	HMEC	breast
48	chr2:63054800-63060400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:63054800-63060800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:63054800-63062600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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