Variant report

Variant	rs6510492
Chromosome Location	chr19:35997363-35997364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:35996502-35999278	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:35997029-35997446	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:35997336-35997519	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:35997262-35997554	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:35997282-35998293	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr19:35997292-35997484	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35996698..35999600-chr19:36003100..36006051,2	MCF-7	breast:
2	chr19:35739927..35742259-chr19:35996033..35997931,2	K562	blood:
3	chr19:35995813..35998806-chr19:36034712..36037823,4	MCF-7	breast:
4	chr19:35991475..35994230-chr19:35996710..35999292,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMKN-1	chr19:35996841-35999459	NONHSAT065857

No data

Variant related genes	Relation type
DMKN	TF binding region
ENSG00000105699	Chromatin interaction
ENSG00000161249	Chromatin interaction
ENSG00000236144	Chromatin interaction
ENSG00000105677	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11084818	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2293700	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs4254439	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4358061	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6510494	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7245699	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	107 gene(s)	inside rSNPs	diseases
4	nsv833811	chr19:35850257-36029535	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6510492	CYP2B7P1	cis	cerebellum	SCAN
rs6510492	POU2F2	cis	cerebellum	SCAN
rs6510492	GGN	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35986400-35999600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:35986400-36000000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:35986400-36000600	Weak transcription	Right Atrium	heart
4	chr19:35986800-36000200	Weak transcription	Gastric	stomach
5	chr19:35986800-36000400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:35987800-35998200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:35988000-35998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:35988000-35999000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:35988000-35999200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:35988200-35997800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:35988200-35998400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr19:35988200-35999000	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr19:35988800-35998600	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr19:35989400-35997600	Strong transcription	Pancreas	Pancrea
15	chr19:35989400-35998800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:35989600-35999200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:35990200-36000400	Weak transcription	Lung	lung
18	chr19:35991000-36000200	Weak transcription	Ovary	ovary
19	chr19:35991200-36000200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:35992200-36000400	Weak transcription	Aorta	Aorta
21	chr19:35992800-35999000	Weak transcription	Hela-S3	cervix
22	chr19:35993200-35999200	Strong transcription	HMEC	breast
23	chr19:35993200-35999400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:35993200-35999600	Weak transcription	Brain Anterior Caudate	brain
25	chr19:35993400-36000000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:35993400-36000200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:35994000-35999000	Strong transcription	NHEK	skin
28	chr19:35994000-35999200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:35994200-35998600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:35994800-35999200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:35996200-35998400	Weak transcription	Esophagus	oesophagus
32	chr19:35996200-35999000	Enhancers	GM12878-XiMat	blood
33	chr19:35996400-35997800	Genic enhancers	HepG2	liver
34	chr19:35996400-35998200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:35996400-35999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:35996600-35997400	Genic enhancers	Fetal Intestine Small	intestine
37	chr19:35997000-35997400	Enhancers	Fetal Intestine Large	intestine
38	chr19:35997200-35999400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr19:35997200-36000000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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