Variant report

Variant	rs35499742
Chromosome Location	chr2:62936454-62936455
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	chr2:62934114..62936851-chr2:63275613..63277785,2	K562	blood:
2	chr2:62731472..62734976-chr2:62932827..62936526,3	K562	blood:

Variant related genes	Relation type
ENSG00000233702	Chromatin interaction
ENSG00000186889	Chromatin interaction
ENSG00000231609	Chromatin interaction
ENSG00000115507	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10208675	0.87[GIH][hapmap]
rs11692262	1.00[CHB][hapmap]
rs12617178	0.82[GIH][hapmap]
rs13030015	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs13398408	0.87[GIH][hapmap]
rs1362311	1.00[ASW][hapmap];0.82[GIH][hapmap];1.00[YRI][hapmap]
rs2049674	1.00[CHB][hapmap]
rs2054835	0.81[AMR][1000 genomes]
rs2539986	0.82[GIH][hapmap]
rs2931488	0.83[CEU][hapmap]
rs2969300	0.83[CEU][hapmap]
rs34503992	0.93[GIH][hapmap];0.91[MEX][hapmap]
rs36009942	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs360786	0.83[CEU][hapmap];0.93[GIH][hapmap]
rs360787	0.81[AMR][1000 genomes]
rs360788	0.81[AMR][1000 genomes]
rs360789	0.81[AMR][1000 genomes]
rs360790	0.81[AMR][1000 genomes]
rs360793	0.83[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs360794	0.83[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs360795	0.83[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs360796	0.83[CEU][hapmap]
rs360798	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]
rs360802	1.00[ASW][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs360805	0.87[GIH][hapmap]
rs360806	0.83[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs6758263	0.81[AMR][1000 genomes]
rs6760804	0.87[GIH][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	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
rs35499742	OTX1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62931800-62938000	Active TSS	Stomach Smooth Muscle	stomach
2	chr2:62933800-62936600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr2:62933800-62938400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:62934200-62936600	Transcr. at gene 5' and 3'	HMEC	breast
5	chr2:62934200-62937400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr2:62934200-62945800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:62934200-62957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:62934200-62957800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:62934400-62937200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:62934400-62938400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:62934400-62939800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:62934400-62957800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:62934600-62936800	Active TSS	Right Atrium	heart
14	chr2:62934600-62937200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr2:62934600-62937600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:62934600-62940600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:62934600-62942200	Weak transcription	Spleen	Spleen
18	chr2:62934600-62943800	Weak transcription	Aorta	Aorta
19	chr2:62934600-62945000	Weak transcription	Right Ventricle	heart
20	chr2:62934600-62945400	Weak transcription	Fetal Thymus	thymus
21	chr2:62934600-62947400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:62934600-62951600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:62934600-62951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:62934600-62951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:62934600-62951800	Weak transcription	Esophagus	oesophagus
26	chr2:62934600-62951800	Weak transcription	Left Ventricle	heart
27	chr2:62934600-62952400	Weak transcription	Gastric	stomach
28	chr2:62934600-62957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:62934600-62957800	Weak transcription	Thymus	Thymus
30	chr2:62934600-62957800	Weak transcription	HSMMtube	muscle
31	chr2:62934800-62936600	Enhancers	Fetal Heart	heart
32	chr2:62934800-62938600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:62934800-62938800	Weak transcription	Fetal Kidney	kidney
34	chr2:62934800-62939200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:62934800-62939600	Strong transcription	HSMM	muscle
36	chr2:62934800-62951800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:62935000-62937000	Weak transcription	Primary B cells from cord blood	blood
38	chr2:62935000-62937400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr2:62935000-62948400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:62935200-62939000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:62935200-62943200	Weak transcription	HUVEC	blood vessel
42	chr2:62935200-62949000	Weak transcription	Fetal Intestine Large	intestine
43	chr2:62935400-62936600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:62935400-62936600	Genic enhancers	K562	blood
45	chr2:62935400-62936800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:62935400-62937000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:62935400-62937000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:62935400-62937000	Transcr. at gene 5' and 3'	Dnd41	blood
49	chr2:62935400-62937200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:62935400-62937400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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