Variant report

Variant	rs7004687
Chromosome Location	chr8:87718095-87718096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10095670	0.87[EUR][1000 genomes]
rs10105388	0.91[EUR][1000 genomes]
rs10106148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504826	1.00[JPT][hapmap]
rs10956936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12334406	0.87[EUR][1000 genomes]
rs13270693	0.80[YRI][hapmap]
rs16917022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28542956	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58212982	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6983426	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6988548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6998478	0.87[EUR][1000 genomes]
rs7000661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7017987	1.00[JPT][hapmap]
rs7814536	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841121	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7845157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297940	1.00[JPT][hapmap]
rs9297961	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers 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 target site	31 gene(s)	inside rSNPs	diseases
2	nsv891151	chr8:87690019-87776019	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1026794	chr8:87698639-87957840	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv539662	chr8:87698639-87957840	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7004687	CNGB3	cis	parietal	SCAN
rs7004687	OSGIN2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87715800-87719200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr8:87716000-87718400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:87716000-87718600	Weak transcription	Osteobl	bone
4	chr8:87716000-87721400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr8:87716000-87721600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:87716200-87718600	Weak transcription	HUVEC	blood vessel
7	chr8:87716400-87718400	Weak transcription	Fetal Brain Female	brain
8	chr8:87717200-87719000	Enhancers	Fetal Stomach	stomach
9	chr8:87717400-87718400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr8:87717400-87721200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr8:87717600-87721600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:87717800-87718600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:87717800-87718600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:87717800-87718800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr8:87717800-87719000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr8:87718000-87718200	Flanking Active TSS	GM12878-XiMat	blood
17	chr8:87718000-87718800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr8:87718000-87718800	Enhancers	Ovary	ovary
19	chr8:87718000-87720200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr8:87718000-87721200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:87718000-87721600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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