Variant report

Variant	rs12713468
Chromosome Location	chr2:62983213-62983214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10153716	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1022110	0.92[CEU][hapmap]
rs11682530	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11688816	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11893131	0.96[CEU][hapmap]
rs12713467	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12989754	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12994674	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13013218	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13418889	0.81[AFR][1000 genomes]
rs1420018	0.92[CEU][hapmap];0.89[ASN][1000 genomes]
rs1553832	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17027429	0.92[CEU][hapmap];0.81[AFR][1000 genomes]
rs1828398	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs189671	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1906198	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2058566	0.87[CEU][hapmap];0.88[ASN][1000 genomes]
rs2080227	0.80[CEU][hapmap];0.84[AFR][1000 genomes]
rs2136737	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2215870	0.96[CEU][hapmap];0.89[ASN][1000 genomes]
rs2421816	0.87[CEU][hapmap]
rs2430388	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2539980	0.83[ASN][1000 genomes]
rs2539985	0.89[ASN][1000 genomes]
rs2539987	0.96[CEU][hapmap]
rs2710637	0.83[CEU][hapmap]
rs2710638	0.88[ASN][1000 genomes]
rs2710639	0.88[CEU][hapmap]
rs2710640	0.89[ASN][1000 genomes]
rs2710642	0.87[CEU][hapmap];0.89[ASN][1000 genomes]
rs34104251	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs360797	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs360799	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs360800	0.96[CEU][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs360801	0.83[CEU][hapmap];0.89[ASN][1000 genomes]
rs360804	0.96[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs360807	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3927201	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4461246	0.96[CEU][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671050	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671051	0.82[EUR][1000 genomes]
rs4671448	0.82[ASN][1000 genomes]
rs4671450	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545971	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6545972	0.92[CEU][hapmap]
rs6545973	0.87[CEU][hapmap]
rs7557501	0.92[CEU][hapmap]
rs7562149	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7562734	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7567923	0.92[CEU][hapmap]
rs7573756	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9678329	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9973612	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62953600-63001200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:62958200-63010200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:62961200-63011600	Weak transcription	NHLF	lung
4	chr2:62967000-62997000	Weak transcription	Dnd41	blood
5	chr2:62968400-62995200	Weak transcription	Left Ventricle	heart
6	chr2:62969800-62987600	Weak transcription	HMEC	breast
7	chr2:62972200-62983600	Weak transcription	Gastric	stomach
8	chr2:62972400-62987600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:62973000-62988800	Weak transcription	Adipose Nuclei	Adipose
10	chr2:62973400-62986800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:62973400-62987600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:62973800-62990800	Weak transcription	Fetal Lung	lung
13	chr2:62974200-63017200	Weak transcription	Primary T cells from cord blood	blood
14	chr2:62975200-62987600	Weak transcription	HSMM	muscle
15	chr2:62975200-62988800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:62975400-62985200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:62976000-62985600	Weak transcription	A549	lung
18	chr2:62980400-62983600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:62982000-62990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:62982200-62984200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:62982200-62987200	Weak transcription	Ovary	ovary
22	chr2:62982200-62987600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:62982200-62987600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:62982200-62987800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:62982200-63009800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:62982200-63033400	Weak transcription	Fetal Intestine Large	intestine
27	chr2:62982400-62984000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:62982400-62984600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:62982400-62985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:62982400-62987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:62982400-62987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:62982400-62987400	Weak transcription	NH-A	brain
33	chr2:62982400-62992800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:62982400-62994400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:62982400-62996000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:62982400-63006200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:62982800-62985600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:62982800-62987000	Weak transcription	Liver	Liver
39	chr2:62983000-62983600	Genic enhancers	HepG2	liver
40	chr2:62983000-62991200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:62983200-62986800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:62983200-62995600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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