Variant report

Variant	rs7562149
Chromosome Location	chr2:63008414-63008415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10153716	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1022110	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11682530	0.93[ASW][hapmap];0.87[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap]
rs11688816	0.93[ASW][hapmap];0.86[LWK][hapmap];0.88[YRI][hapmap]
rs11893131	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713467	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12713468	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12989754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12994674	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13013218	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13398408	0.88[YRI][hapmap]
rs13410889	0.83[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs13418889	0.81[ASN][1000 genomes]
rs1420018	0.87[CEU][hapmap]
rs1468748	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1553832	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17027429	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1828398	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877026	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs189671	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1906198	0.92[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2058566	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs2058567	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2080227	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs2136737	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2215870	0.92[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs2421816	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2430388	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs2539978	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs2539984	0.86[ASN][1000 genomes]
rs2539987	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[LWK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap]
rs2710637	0.85[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs2710638	0.80[YRI][hapmap]
rs2710639	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2710640	0.81[EUR][1000 genomes]
rs2710642	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs34104251	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360797	0.86[ASW][hapmap];0.88[CEU][hapmap];0.90[GIH][hapmap];0.88[YRI][hapmap]
rs360799	0.91[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.81[EUR][1000 genomes]
rs360800	0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs360801	0.88[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs360804	0.92[CEU][hapmap];0.87[GIH][hapmap]
rs360807	0.86[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[YRI][hapmap]
rs3927201	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4461246	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4671050	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671051	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671450	0.90[EUR][1000 genomes]
rs6545971	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs6545972	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545973	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6714241	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7557501	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7562734	0.85[EUR][1000 genomes]
rs7567923	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7571916	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7573756	0.86[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7591708	0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs9678329	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9789661	0.80[ASN][1000 genomes]
rs9973612	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7562149	COMMD1	cis	cerebellum	SCAN
rs7562149	VPS54	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62958200-63010200	Weak transcription	Primary B cells from cord blood	blood
2	chr2:62961200-63011600	Weak transcription	NHLF	lung
3	chr2:62974200-63017200	Weak transcription	Primary T cells from cord blood	blood
4	chr2:62982200-63009800	Weak transcription	Fetal Intestine Small	intestine
5	chr2:62982200-63033400	Weak transcription	Fetal Intestine Large	intestine
6	chr2:62984400-63009800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:62988000-63009600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:62988000-63010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:62988000-63012400	Weak transcription	HSMM	muscle
10	chr2:62988200-63012400	Weak transcription	HMEC	breast
11	chr2:62994800-63010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:63000800-63009200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:63001800-63010200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:63002000-63009200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:63002000-63010200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:63002200-63011600	Weak transcription	NHDF-Ad	bronchial
17	chr2:63002200-63012400	Weak transcription	NH-A	brain
18	chr2:63002200-63016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:63002600-63012000	Weak transcription	NHEK	skin
20	chr2:63002600-63013200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:63003000-63012200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:63003400-63009000	Strong transcription	HepG2	liver
23	chr2:63005200-63009800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:63005200-63010200	Weak transcription	Adipose Nuclei	Adipose
25	chr2:63005400-63010200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:63005600-63010200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:63005600-63010200	Weak transcription	Esophagus	oesophagus
28	chr2:63005600-63010600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:63005600-63012400	Weak transcription	Liver	Liver
30	chr2:63005800-63010200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:63006200-63008600	Strong transcription	A549	lung
32	chr2:63006400-63010600	Weak transcription	Pancreas	Pancrea
33	chr2:63006600-63009800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:63006800-63010200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:63007000-63011000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:63007400-63009200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:63007600-63010800	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:63007600-63013200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:63008200-63008800	Enhancers	Ovary	ovary

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