Variant report

Variant	rs1931990
Chromosome Location	chr6:142597120-142597121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1475772	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1931989	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2328322	0.86[ASN][1000 genomes]
rs2782533	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2782538	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2795303	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2795306	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7745188	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs9321859	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs9484606	0.81[ASN][1000 genomes]
rs9496306	0.85[ASN][1000 genomes]
rs9496309	0.90[CHB][hapmap];0.86[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1029666	chr6:142594099-142643084	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1931990	CITED2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142595000-142597200	Enhancers	Fetal Intestine Large	intestine
2	chr6:142595000-142597600	Enhancers	Fetal Intestine Small	intestine
3	chr6:142595600-142598400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:142596000-142597200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:142596000-142597400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:142596000-142600800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:142596400-142597200	Enhancers	HepG2	liver
8	chr6:142596400-142597400	Enhancers	Placenta	Placenta
9	chr6:142596800-142597200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr6:142596800-142597200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr6:142596800-142597200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:142596800-142597200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:142596800-142597200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:142596800-142597200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:142597000-142597400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:142597000-142597400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:142597000-142597800	Enhancers	A549	lung
18	chr6:142597000-142597800	Enhancers	HUVEC	blood vessel
19	chr6:142597000-142600200	Weak transcription	NHEK	skin

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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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