Variant report

Variant	rs4802070
Chromosome Location	chr19:40726336-40726337
allele	A/G
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	FOSL2	chr19:40725204-40726345	A549	lung:	n/a	chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
2	MAX	chr19:40725148-40726431	A549	lung:	n/a	chr19:40725924-40725933
3	JUND	chr19:40725327-40726683	HCT-116	colon:	n/a	chr19:40725947-40725958 chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
4	USF1	chr19:40725431-40726428	HCT-116	colon:	n/a	chr19:40725923-40725934
5	REST	chr19:40721682-40727491	PANC-1	pancreas:	n/a	chr19:40721931-40721944 chr19:40726153-40726161
6	POLR2A	chr19:40725203-40726430	PFSK-1	brain:	n/a	n/a
7	USF1	chr19:40725370-40726361	HCT-116	colon:	n/a	chr19:40725923-40725934
8	SP1	chr19:40725385-40726404	A549	lung:	n/a	n/a
9	REST	chr19:40721744-40727478	PANC-1	pancreas:	n/a	chr19:40721931-40721944 chr19:40726153-40726161
10	REST	chr19:40725106-40729998	PANC-1	pancreas:	n/a	chr19:40726153-40726161
11	SRF	chr19:40725151-40726439	HCT-116	colon:	n/a	n/a
12	BCL3	chr19:40725250-40726532	A549	lung:	n/a	n/a
13	USF1	chr19:40725563-40726340	ECC-1	luminal epithelium:	n/a	chr19:40725923-40725934
14	FOSL1	chr19:40725255-40726564	HCT-116	colon:	n/a	chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
15	POLR2A	chr19:40725000-40726351	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40724342..40727794-chr19:40739430..40743149,3	K562	blood:
2	chr19:40719578..40724896-chr19:40726262..40733162,10	MCF-7	breast:
3	chr19:40721117..40723953-chr19:40725760..40727528,2	K562	blood:

Variant related genes	Relation type
TTC9B	TF binding region
ENSG00000174521	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10402740	0.87[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1129156	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668242	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs11880261	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs12971806	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12975651	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189281	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304189	0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2356229	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339522	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339523	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339525	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339526	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3730050	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap]
rs3730051	0.85[CHB][hapmap];0.93[MEX][hapmap]
rs3746005	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4239504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4257318	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap]
rs4337402	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4490099	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4530264	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4558508	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap]
rs4802071	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4802073	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4802074	0.87[MEX][hapmap]
rs4803320	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56694147	0.83[ASN][1000 genomes]
rs6508936	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7247201	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249146	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs7250897	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap]
rs7252471	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7257972	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7258548	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7260249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260517	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap]
rs8100018	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8102171	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap]
rs8106744	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110888	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs969531	0.84[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap]
rs9749056	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv911703	chr19:40711333-40730279	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv911704	chr19:40716652-40730279	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv911705	chr19:40716652-40731371	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4802070	GRIN2D	cis	cerebellum	SCAN
rs4802070	ZNF229	cis	cerebellum	SCAN
rs4802070	SPACA4	cis	cerebellum	SCAN
rs4802070	C19orf47	cis	lymphoblastoid	seeQTL
rs4802070	IGFL4	cis	parietal	SCAN
rs4802070	ZNF221	cis	cerebellum	SCAN
rs4802070	C19orf47	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
2	chr19:40723800-40729000	Weak transcription	Gastric	stomach
3	chr19:40724200-40729000	Weak transcription	Pancreas	Pancrea
4	chr19:40725200-40726400	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr19:40725200-40726400	Enhancers	K562	blood
6	chr19:40725400-40727000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:40725600-40726400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr19:40725800-40726400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:40726000-40726400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:40726000-40726400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:40726000-40726400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:40726000-40726400	Bivalent Enhancer	Fetal Intestine Small	intestine
13	chr19:40726000-40726400	Enhancers	HUVEC	blood vessel
14	chr19:40726000-40726400	Enhancers	NH-A	brain
15	chr19:40726000-40726400	Enhancers	NHEK	skin
16	chr19:40726000-40726400	Enhancers	Osteobl	bone
17	chr19:40726000-40731600	Weak transcription	NHLF	lung
18	chr19:40726200-40726400	Enhancers	A549	lung
19	chr19:40726200-40726400	Enhancers	Hela-S3	cervix
20	chr19:40726200-40731400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:40726200-40731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:40726200-40731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:40726200-40731600	Weak transcription	NHDF-Ad	bronchial

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