Variant report

Variant	rs13398408
Chromosome Location	chr2:62987735-62987736
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62970786..62972679-chr2:62986051..62988226,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10208675	1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[ASN][1000 genomes]
rs1038570	0.89[CHD][hapmap]
rs11682530	0.84[YRI][hapmap]
rs11688816	0.92[YRI][hapmap]
rs11893131	0.84[YRI][hapmap]
rs11900596	0.85[ASN][1000 genomes]
rs12617178	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs12989754	0.88[YRI][hapmap]
rs13003895	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013218	0.96[YRI][hapmap]
rs1362311	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs1386400	0.89[CHD][hapmap]
rs17027429	0.92[YRI][hapmap]
rs181723	0.91[ASN][1000 genomes]
rs1828398	0.83[YRI][hapmap]
rs2054835	0.91[ASN][1000 genomes]
rs2080227	0.92[YRI][hapmap]
rs2430388	0.91[YRI][hapmap]
rs2539979	0.91[ASN][1000 genomes]
rs2539986	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs2553042	0.91[ASN][1000 genomes]
rs2710635	0.87[ASN][1000 genomes]
rs2710638	0.83[YRI][hapmap]
rs2901518	0.91[ASN][1000 genomes]
rs2931488	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2969300	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs34503992	0.89[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs35499742	0.87[GIH][hapmap]
rs36009942	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs360786	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360787	0.91[ASN][1000 genomes]
rs360788	0.91[ASN][1000 genomes]
rs360789	0.91[ASN][1000 genomes]
rs360790	0.91[ASN][1000 genomes]
rs360793	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs360794	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs360795	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs360796	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs360797	0.92[YRI][hapmap]
rs360798	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360799	0.82[YRI][hapmap]
rs360802	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360806	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs360807	0.92[YRI][hapmap]
rs36193012	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4461246	0.96[YRI][hapmap]
rs4671050	0.90[MKK][hapmap];0.96[YRI][hapmap]
rs56065771	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545971	0.87[YRI][hapmap]
rs6545972	0.84[YRI][hapmap]
rs6745862	0.81[ASN][1000 genomes]
rs6758263	0.91[ASN][1000 genomes]
rs6760804	0.82[CHD][hapmap];0.87[GIH][hapmap];0.85[ASN][1000 genomes]
rs67657712	0.89[ASN][1000 genomes]
rs7557501	0.92[YRI][hapmap]
rs7562149	0.88[YRI][hapmap]
rs7567923	0.92[YRI][hapmap]
rs7573756	0.80[MKK][hapmap];0.92[YRI][hapmap]
rs7590973	0.85[ASN][1000 genomes]
rs9973612	0.88[YRI][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13398408	OTX1	cis	cerebellum	SCAN

Chromatin state (count:44 , 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	chr2:62973000-62988800	Weak transcription	Adipose Nuclei	Adipose
7	chr2:62973800-62990800	Weak transcription	Fetal Lung	lung
8	chr2:62974200-63017200	Weak transcription	Primary T cells from cord blood	blood
9	chr2:62975200-62988800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:62982000-62990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:62982200-62987800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:62982200-63009800	Weak transcription	Fetal Intestine Small	intestine
13	chr2:62982200-63033400	Weak transcription	Fetal Intestine Large	intestine
14	chr2:62982400-62992800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:62982400-62994400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:62982400-62996000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:62982400-63006200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:62983000-62991200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:62983200-62995600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:62984400-63009800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:62985400-62991400	Genic enhancers	HepG2	liver
22	chr2:62986600-62987800	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:62986800-62987800	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr2:62987000-62987800	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:62987000-62988800	Enhancers	A549	lung
26	chr2:62987200-62987800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:62987200-62988000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:62987200-62988400	Enhancers	Osteobl	bone
29	chr2:62987200-62988600	Enhancers	NHDF-Ad	bronchial
30	chr2:62987400-62987800	Weak transcription	Ovary	ovary
31	chr2:62987400-62988000	Enhancers	NHEK	skin
32	chr2:62987400-62988200	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:62987400-62988200	Enhancers	Stomach Mucosa	stomach
34	chr2:62987400-62988200	Enhancers	NH-A	brain
35	chr2:62987400-62993000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:62987600-62987800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:62987600-62988000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:62987600-62988000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:62987600-62988000	Enhancers	HSMM	muscle
40	chr2:62987600-62988200	Enhancers	HMEC	breast
41	chr2:62987600-62988400	Weak transcription	Liver	Liver
42	chr2:62987600-62988600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:62987600-62988600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr2:62987600-62989000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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