Variant report

Variant	rs9874641
Chromosome Location	chr3:139039254-139039255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139035215..139036963-chr3:139038914..139040454,2	K562	blood:
2	chr3:139033989..139036963-chr3:139038914..139041363,3	K562	blood:
3	chr3:139029076..139033479-chr3:139037377..139040244,5	K562	blood:
4	chr3:138999143..139001318-chr3:139037402..139040316,2	K562	blood:
5	chr3:138823453..138825465-chr3:139037865..139040237,2	K562	blood:
6	chr3:139038395..139039373-chr3:139047948..139048735,2	MCF-7	breast:
7	chr3:139037501..139040197-chr3:139041266..139044238,3	K562	blood:
8	chr3:139038837..139041426-chr3:139046835..139048335,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12695695	1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.80[AMR][1000 genomes]
rs34654084	0.89[AMR][1000 genomes]
rs9839834	0.83[AMR][1000 genomes]
rs9846449	1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.83[AMR][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	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
2	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9874641	ATP1B3	cis	cerebellum	SCAN
rs9874641	BPESC1	cis	cerebellum	SCAN
rs9874641	COPB2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139032400-139048000	Weak transcription	Right Atrium	heart
2	chr3:139035600-139041200	Enhancers	K562	blood
3	chr3:139037000-139041200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:139037000-139041600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:139037400-139044200	Weak transcription	Pancreas	Pancrea
6	chr3:139037400-139047800	Weak transcription	NHDF-Ad	bronchial
7	chr3:139037600-139039400	Weak transcription	A549	lung
8	chr3:139037800-139047600	Weak transcription	Hela-S3	cervix
9	chr3:139038400-139048000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:139038800-139039600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:139038800-139039800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:139039000-139039400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:139039000-139039400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:139039000-139039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:139039200-139039600	Enhancers	Ovary	ovary

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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

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