Variant report

Variant	rs360798
Chromosome Location	chr2:62950435-62950436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62931865..62934315-chr2:62945746..62950765,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10208675	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs1038570	0.89[CHD][hapmap]
rs11900596	0.85[ASN][1000 genomes]
rs12617178	0.94[CEU][hapmap];0.88[GIH][hapmap]
rs13003895	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030015	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[YRI][hapmap]
rs13398408	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]
rs1362311	1.00[ASW][hapmap];0.94[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs1386400	0.89[CHD][hapmap]
rs181723	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2054835	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2539979	0.91[ASN][1000 genomes]
rs2539986	0.94[CEU][hapmap];0.88[GIH][hapmap]
rs2553042	0.91[ASN][1000 genomes]
rs2710635	0.87[ASN][1000 genomes]
rs2901518	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2931488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2969300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34503992	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs35499742	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs36009942	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs360786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360787	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360788	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360789	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360790	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs360794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360802	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360805	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36193012	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56065771	0.81[ASN][1000 genomes]
rs6745862	0.81[ASN][1000 genomes]
rs6758263	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6760804	0.84[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs67657712	0.89[ASN][1000 genomes]
rs7590973	0.85[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs360798	OTX1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62934200-62957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:62934200-62957800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:62934400-62957800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:62934600-62951600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:62934600-62951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:62934600-62951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:62934600-62951800	Weak transcription	Esophagus	oesophagus
8	chr2:62934600-62951800	Weak transcription	Left Ventricle	heart
9	chr2:62934600-62952400	Weak transcription	Gastric	stomach
10	chr2:62934600-62957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:62934600-62957800	Weak transcription	Thymus	Thymus
12	chr2:62934600-62957800	Weak transcription	HSMMtube	muscle
13	chr2:62934800-62951800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:62935800-62957800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:62936000-62951800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:62936200-62957800	Weak transcription	Small Intestine	intestine
17	chr2:62936400-62951400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:62936400-62951800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:62936400-62957800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:62936400-62957800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:62936600-62951800	Weak transcription	Pancreas	Pancrea
22	chr2:62936600-62957800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:62936600-62957800	Weak transcription	Hela-S3	cervix
24	chr2:62937200-62951400	Weak transcription	Fetal Heart	heart
25	chr2:62937200-62957800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:62937200-62957800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:62937400-62957800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:62938000-62951600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:62938600-62957800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:62939400-62951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:62939400-62952200	Weak transcription	Fetal Brain Male	brain
32	chr2:62939600-62952400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:62939800-62952200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:62940000-62952800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:62941800-62951800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:62941800-62957800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:62943800-62952200	Weak transcription	Osteobl	bone
38	chr2:62944000-62951400	Weak transcription	Adipose Nuclei	Adipose
39	chr2:62944000-62951800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:62944000-62952200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:62944000-62957800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:62944000-62957800	Weak transcription	Aorta	Aorta
43	chr2:62944200-62951400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:62944200-62951800	Weak transcription	Fetal Stomach	stomach
45	chr2:62944200-62952600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:62944200-62957800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:62944400-62957800	Weak transcription	NHEK	skin
48	chr2:62944600-62951400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:62944600-62951400	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:62944600-62951800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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