Variant report

Variant	rs6802174
Chromosome Location	chr3:139006664-139006665
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10212419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12695694	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853827	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9866054	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591856	chr3:139000844-139037832	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6802174	SPSB4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138999000-139006800	Weak transcription	Pancreas	Pancrea
2	chr3:139000800-139011200	Weak transcription	NHLF	lung
3	chr3:139002000-139011600	Weak transcription	HSMM	muscle
4	chr3:139003200-139007000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:139003600-139009200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:139004400-139007200	Enhancers	K562	blood
7	chr3:139004400-139008200	Enhancers	Ovary	ovary
8	chr3:139004600-139008000	Enhancers	Right Ventricle	heart
9	chr3:139005000-139008000	Enhancers	Left Ventricle	heart
10	chr3:139005400-139008400	Enhancers	Fetal Heart	heart
11	chr3:139005600-139007200	Weak transcription	Right Atrium	heart
12	chr3:139005800-139007200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:139006000-139007600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:139006200-139007400	Weak transcription	Spleen	Spleen
15	chr3:139006400-139006800	Weak transcription	Fetal Lung	lung
16	chr3:139006600-139007000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:139006600-139007600	Enhancers	Placenta	Placenta
18	chr3:139006600-139008000	Enhancers	NHDF-Ad	bronchial
19	chr3:139006600-139008200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

Quick Search:

Input of quick search could be:

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

what's new

Quick links