Variant report

Variant	rs34392719
Chromosome Location	chr3:142342112-142342113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:142342093-142342303	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr3:142342020-142342383	MCF-7	breast:	n/a	n/a
3	CEBPB	chr3:142341994-142342328	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr3:142342085-142342379	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr3:142342070-142342215	A549	lung:	n/a	n/a
6	GATA3	chr3:142341858-142342516	MCF-7	breast:	n/a	chr3:142342379-142342395 chr3:142342384-142342394
7	EP300	chr3:142342065-142342285	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PLS1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11718899	0.85[EUR][1000 genomes]
rs11916455	0.85[CEU][hapmap]
rs11917460	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11928203	0.89[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs13070239	0.85[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap]
rs13071750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074153	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13078890	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13085261	0.85[CEU][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap]
rs13091247	0.81[ASN][1000 genomes]
rs13093304	0.84[EUR][1000 genomes]
rs13099184	0.82[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap]
rs2049326	0.89[CHB][hapmap]
rs2140437	0.89[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2354858	0.89[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34372236	0.83[ASN][1000 genomes]
rs4256152	0.85[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs4582075	0.85[CEU][hapmap]
rs4594656	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs4683427	0.89[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs62278480	0.81[ASN][1000 genomes]
rs6809448	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7432464	0.85[EUR][1000 genomes]
rs9829125	0.82[TSI][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	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34392719	XRN1	cis	cerebellum	SCAN
rs34392719	TRPC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142334000-142357200	Weak transcription	Pancreas	Pancrea
2	chr3:142337800-142348400	Weak transcription	Gastric	stomach
3	chr3:142338000-142344200	Weak transcription	Colonic Mucosa	Colon
4	chr3:142338600-142343800	Weak transcription	HSMMtube	muscle
5	chr3:142339400-142342600	Enhancers	Duodenum Mucosa	Duodenum
6	chr3:142340200-142345600	Weak transcription	A549	lung
7	chr3:142340600-142342800	Enhancers	Fetal Intestine Large	intestine
8	chr3:142340600-142343400	Enhancers	Fetal Intestine Small	intestine
9	chr3:142341000-142343200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:142341400-142346200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:142341800-142342400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:142341800-142342400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:142341800-142342400	Enhancers	Small Intestine	intestine
14	chr3:142341800-142342600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr3:142341800-142343600	Enhancers	Stomach Mucosa	stomach

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