Variant report

Variant	rs934426
Chromosome Location	chr19:40731371-40731372
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr19:40731136-40743299	PANC-1	pancreas:	n/a	n/a
2	MAX	chr19:40730018-40731567	HCT-116	colon:	n/a	n/a
3	ELF1	chr19:40731366-40731721	K562	blood:	n/a	chr19:40731534-40731547
4	CTCF	chr19:40731340-40731490	A549	lung:	n/a	n/a
5	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a
6	REST	chr19:40731178-40733034	PANC-1	pancreas:	n/a	chr19:40732699-40732708 chr19:40732184-40732197
7	POLR2A	chr19:40731289-40733027	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:40730457..40732107-chr19:40746793..40748406,2	MCF-7	breast:
2	chr19:40730620..40735723-chr19:40738673..40743679,8	MCF-7	breast:
3	chr19:40728036..40729560-chr19:40729917..40732586,2	K562	blood:
4	chr19:40730680..40732953-chr19:40742312..40745155,2	K562	blood:
5	chr19:40723230..40725206-chr19:40730553..40733160,2	MCF-7	breast:
6	chr19:40730135..40732831-chr19:40769478..40772203,2	MCF-7	breast:
7	chr19:40719578..40724896-chr19:40726262..40733162,10	MCF-7	breast:
8	chr19:40731324..40733318-chr19:40786434..40789035,2	MCF-7	breast:

No data

Variant related genes	Relation type
CNTD2	TF binding region
ENSG00000174521	Chromatin interaction
ENSG00000105219	Chromatin interaction
ENSG00000207631	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10408356	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10415181	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10416620	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10418932	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10419465	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10422343	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs12151243	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap]
rs16974157	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2163840	0.83[ASN][1000 genomes]
rs2304185	0.82[ASN][1000 genomes]
rs2304188	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28362958	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34716810	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55862427	0.80[ASN][1000 genomes]
rs58336440	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59010363	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59343080	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61685259	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62107590	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62107593	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62107594	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7248861	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7254617	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8111619	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs892118	1.00[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs892119	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs892120	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304588	1.00[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304589	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs934426	RPL18	cis	parietal	SCAN
rs934426	EML2	cis	cerebellum	SCAN
rs934426	DEDD2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
2	chr19:40726000-40731600	Weak transcription	NHLF	lung
3	chr19:40726200-40731400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:40726200-40731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:40726200-40731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:40726200-40731600	Weak transcription	NHDF-Ad	bronchial
7	chr19:40726400-40731600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:40726400-40731600	Weak transcription	A549	lung
9	chr19:40726400-40735200	Weak transcription	K562	blood
10	chr19:40728000-40731600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:40729400-40732000	Weak transcription	Gastric	stomach
12	chr19:40729600-40731600	Weak transcription	Lung	lung
13	chr19:40729600-40732000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:40730600-40732000	Enhancers	Hela-S3	cervix
15	chr19:40730800-40731400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:40730800-40731400	Enhancers	NHEK	skin
17	chr19:40730800-40731800	Enhancers	Liver	Liver
18	chr19:40730800-40732000	Weak transcription	Right Ventricle	heart
19	chr19:40731000-40731400	Weak transcription	Spleen	Spleen
20	chr19:40731200-40731400	Bivalent Enhancer	HepG2	liver
21	chr19:40731200-40731600	Weak transcription	Placenta	Placenta

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