Variant report

Variant	rs1990608
Chromosome Location	chr2:40535403-40535404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11888123	0.96[CEU][hapmap]
rs11904139	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13001457	0.82[CEU][hapmap]
rs1477001	0.80[ASN][1000 genomes]
rs2110744	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160236	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2160237	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952402	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544315	0.85[ASN][1000 genomes]
rs6544316	0.85[ASN][1000 genomes]
rs6544317	0.85[ASN][1000 genomes]
rs6544318	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748881	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs727477	0.83[CEU][hapmap]
rs759384	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs998260	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	nsv1010508	chr2:40526981-40590777	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv535655	chr2:40526981-40590777	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40518200-40540600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40528800-40541400	Weak transcription	Dnd41	blood
3	chr2:40530200-40536200	Enhancers	Fetal Heart	heart
4	chr2:40531800-40542600	Weak transcription	Osteobl	bone
5	chr2:40532000-40544800	Weak transcription	HSMM	muscle
6	chr2:40532000-40551800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:40532200-40542400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:40533200-40537400	Weak transcription	Left Ventricle	heart
9	chr2:40533800-40543800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:40534000-40537400	Weak transcription	Right Ventricle	heart
11	chr2:40534000-40543000	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:40534400-40535800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:40535000-40537400	Weak transcription	Right Atrium	heart
14	chr2:40535200-40536000	Enhancers	Fetal Intestine Large	intestine
15	chr2:40535200-40536200	Enhancers	Fetal Intestine Small	intestine
16	chr2:40535400-40535600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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