Variant report

Variant	rs7593406
Chromosome Location	chr2:40475441-40475442
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10180584	0.87[ASN][1000 genomes]
rs10490208	0.90[CHD][hapmap];0.80[GIH][hapmap]
rs11124737	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17504670	0.91[CHD][hapmap];0.84[JPT][hapmap]
rs4581943	0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952401	0.91[CHD][hapmap];0.84[JPT][hapmap]
rs4952594	0.94[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs4952599	0.93[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs56410612	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6716847	0.88[ASN][1000 genomes]
rs6737759	0.87[ASN][1000 genomes]
rs7602176	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs877099	0.93[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs918050	0.86[CHB][hapmap];0.94[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7593406	THADA	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr2:40470400-40481200	Weak transcription	Brain Germinal Matrix	brain
6	chr2:40472200-40478600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:40472400-40475800	Weak transcription	Hela-S3	cervix
8	chr2:40472400-40478400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:40472600-40477800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:40472600-40487200	Weak transcription	HSMM	muscle
11	chr2:40472800-40478400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:40474000-40476600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:40474000-40477800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:40474200-40475600	Enhancers	Stomach Smooth Muscle	stomach
15	chr2:40474400-40477200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:40474400-40478400	Weak transcription	Right Ventricle	heart
17	chr2:40474600-40478000	Weak transcription	Fetal Stomach	stomach
18	chr2:40475000-40475800	Enhancers	Fetal Intestine Large	intestine
19	chr2:40475200-40475800	Flanking Active TSS	Fetal Heart	heart
20	chr2:40475200-40475800	Enhancers	Left Ventricle	heart
21	chr2:40475400-40475600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:40475400-40475800	Enhancers	Right Atrium	heart
23	chr2:40475400-40476000	Enhancers	Fetal Intestine Small	intestine
24	chr2:40475400-40476200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr2:40475400-40477200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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