Variant report

Variant	rs380590
Chromosome Location	chr2:40473347-40473348
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40472223..40475000-chr2:40477866..40479502,2	K562	blood:

Variant related genes	Relation type
ENSG00000227028	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1012311	0.91[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs10197174	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10490209	0.98[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12612349	0.97[EUR][1000 genomes]
rs1617492	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1627626	0.82[ASN][1000 genomes]
rs1641454	0.86[EUR][1000 genomes]
rs17025367	0.81[CEU][hapmap]
rs17025588	0.80[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs17025712	0.82[GIH][hapmap]
rs2072530	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs2540904	0.80[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs28421555	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs369251	0.83[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs371492	0.80[JPT][hapmap]
rs376303	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs376535	0.81[CHD][hapmap];0.82[GIH][hapmap]
rs381610	0.82[GIH][hapmap]
rs384673	0.88[EUR][1000 genomes]
rs385341	0.81[CHD][hapmap]
rs390145	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs392317	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392953	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs395987	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs404214	0.80[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs404226	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs407148	0.80[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs408263	0.91[CEU][hapmap];0.80[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs426140	0.90[ASN][1000 genomes]
rs436245	0.81[JPT][hapmap]
rs447136	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs450450	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs62150777	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873912	chr2:40468418-40492315	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873913	chr2:40469705-40485074	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs380590	VIT	cis	parietal	SCAN
rs380590	CCDC75	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40451400-40490000	Weak transcription	Dnd41	blood
3	chr2:40467800-40487400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:40468000-40476600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:40469000-40475200	Enhancers	Fetal Heart	heart
6	chr2:40469800-40474400	Enhancers	Rectal Smooth Muscle	rectum
7	chr2:40470400-40481200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:40470800-40474800	Enhancers	Fetal Intestine Small	intestine
9	chr2:40471200-40474600	Enhancers	Fetal Intestine Large	intestine
10	chr2:40471200-40474600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:40472000-40473400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:40472000-40473400	Weak transcription	Fetal Stomach	stomach
13	chr2:40472000-40473600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:40472000-40473600	Weak transcription	Right Ventricle	heart
15	chr2:40472200-40473600	Weak transcription	Left Ventricle	heart
16	chr2:40472200-40474400	Weak transcription	Fetal Lung	lung
17	chr2:40472200-40478600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:40472400-40473600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:40472400-40475800	Weak transcription	Hela-S3	cervix
20	chr2:40472400-40478400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:40472600-40473600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:40472600-40473600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:40472600-40475400	Weak transcription	Right Atrium	heart
24	chr2:40472600-40477800	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:40472600-40487200	Weak transcription	HSMM	muscle
26	chr2:40472800-40473400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:40472800-40474200	Weak transcription	Osteobl	bone
28	chr2:40472800-40478400	Weak transcription	Rectal Mucosa Donor 31	rectum

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