Variant report

Variant	rs316623
Chromosome Location	chr15:41801081-41801082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1077809	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10851405	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070331	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1200340	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1200345	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs1200348	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs1200349	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs1867419	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2253936	0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2274858	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs2289739	0.82[ASW][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs2289740	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2297377	0.89[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2297378	0.85[CHB][hapmap]
rs2777490	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs316622	1.00[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3759793	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035331	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8035575	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv569233	chr15:41784809-41805237	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv33378	chr15:41786505-41805760	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs316623	SPINT1	cis	parietal	SCAN
rs316623	NDUFAF1	cis	lymphoblastoid	seeQTL
rs316623	RPAP1	cis	lymphoblastoid	seeQTL
rs316623	NDUFAF1	cis	parietal	SCAN
rs316623	RPAP1	cis	multi-tissue	Pritchard
rs316623	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs316623	SPTBN5	cis	parietal	SCAN
rs316623	RPAP1	cis	parietal	SCAN
rs316623	BUB1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41789400-41802600	Weak transcription	K562	blood
2	chr15:41795400-41803600	Weak transcription	Lung	lung
3	chr15:41795400-41804200	Weak transcription	Right Atrium	heart
4	chr15:41795600-41801200	Strong transcription	Fetal Intestine Small	intestine
5	chr15:41798200-41803000	Weak transcription	Spleen	Spleen
6	chr15:41798800-41801600	Enhancers	Stomach Mucosa	stomach
7	chr15:41799000-41801600	Enhancers	Duodenum Mucosa	Duodenum
8	chr15:41799400-41801400	Enhancers	Colonic Mucosa	Colon
9	chr15:41800000-41801200	Enhancers	Pancreas	Pancrea
10	chr15:41800400-41801400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr15:41800400-41803400	Weak transcription	Gastric	stomach
12	chr15:41800800-41801400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr15:41800800-41801600	Flanking Active TSS	Hela-S3	cervix
14	chr15:41801000-41801200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
15	chr15:41801000-41801400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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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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