Variant report

Variant	rs9261434
Chromosome Location	chr6:30087776-30087777
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs2240069	0.82[EUR][1000 genomes]
rs3094068	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3094079	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130397	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3132122	0.82[EUR][1000 genomes]
rs3132123	0.82[EUR][1000 genomes]
rs3132675	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3132676	0.91[ASN][1000 genomes]
rs3132678	0.82[EUR][1000 genomes]
rs3132679	0.80[EUR][1000 genomes]
rs4959045	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763159	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261402	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261494	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261547	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9261588	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv884055	chr6:30078275-30087776	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv601476	chr6:30085838-30091311	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9261434	ZKSCAN3	cis	cerebellum	SCAN
rs9261434	PRSS16	cis	parietal	SCAN
rs9261434	HCG22	cis	lymphoblastoid	seeQTL
rs9261434	FLJ35429	cis	multi-tissue	Pritchard
rs9261434	BTN3A3	cis	parietal	SCAN
rs9261434	HLA-F	cis	multi-tissue	Pritchard
rs9261434	HLA-H	cis	multi-tissue	Pritchard
rs9261434	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30082000-30089400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:30082400-30091000	Weak transcription	HepG2	liver
3	chr6:30086200-30088000	Enhancers	Fetal Intestine Large	intestine
4	chr6:30086200-30092600	Enhancers	Fetal Intestine Small	intestine
5	chr6:30086400-30088000	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr6:30087200-30088000	Enhancers	Hela-S3	cervix
7	chr6:30087200-30088000	Enhancers	NHDF-Ad	bronchial
8	chr6:30087400-30088000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr6:30087400-30088200	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr6:30087400-30090600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:30087600-30089200	Weak transcription	Colonic Mucosa	Colon
12	chr6:30087600-30089400	Weak transcription	Stomach Mucosa	stomach
13	chr6:30087600-30089600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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