Variant report

Variant	rs2283617
Chromosome Location	chr19:18706504-18706505
allele	A/G
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:11)
LncRNA
region (count:0)
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	chr19:18706473-18706687	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:18706286-18706600	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:18705070-18706900	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:18706292-18706889	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:18706286-18706527	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:18706493-18706652	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18704422..18706630-chr19:18794126..18796450,2	K562	blood:
2	chr19:18703681..18707981-chr19:18746387..18750076,5	K562	blood:
3	chr19:18653590..18656982-chr19:18704077..18706738,3	K562	blood:
4	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
5	chr19:18704569..18706809-chr19:18943109..18944717,2	K562	blood:
6	chr19:18705236..18708147-chr19:18708992..18711198,3	K562	blood:
7	chr19:18704422..18706630-chr19:18794126..18797351,3	K562	blood:
8	chr19:18706092..18707788-chr19:18746587..18749190,2	K562	blood:
9	chr19:18534817..18537045-chr19:18704121..18707068,2	MCF-7	breast:
10	chr19:18705427..18706927-chr2:10498314..10500918,2	K562	blood:
11	chr19:18631279..18634372-chr19:18705678..18709198,3	K562	blood:

No data

Variant related genes	Relation type
CRLF1	TF binding region
ENSG00000006016	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000268983	Chromatin interaction
ENSG00000105662	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11668617	0.86[CHD][hapmap]
rs12461284	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2002632	0.82[ASN][1000 genomes]
rs2074177	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2238647	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2314662	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3761031	0.84[ASN][1000 genomes]
rs4808822	0.80[CEU][hapmap]
rs4808828	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7246833	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249956	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252535	0.83[ASN][1000 genomes]
rs7253677	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109611	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110573	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs889363	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv911288	chr19:18700047-18739497	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv911290	chr19:18701499-18720981	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
12	nsv911291	chr19:18701499-18726856	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
13	nsv911292	chr19:18701499-18731658	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2283617	ZNF682	cis	parietal	SCAN
rs2283617	UBA52	cis	lymphoblastoid	seeQTL
rs2283617	INSL3	cis	cerebellum	SCAN
rs2283617	ISYNA1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18701200-18713600	Weak transcription	HSMMtube	muscle
2	chr19:18702200-18707600	Weak transcription	Gastric	stomach
3	chr19:18703200-18707800	Weak transcription	Lung	lung
4	chr19:18704400-18706800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:18705600-18706600	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr19:18705600-18706600	Bivalent Enhancer	Fetal Lung	lung
7	chr19:18705600-18706800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:18705600-18707000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr19:18705600-18707200	Weak transcription	Hela-S3	cervix
10	chr19:18705800-18706600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
11	chr19:18705800-18706600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr19:18705800-18706600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:18705800-18706600	Enhancers	Primary B cells from peripheral blood	blood
14	chr19:18705800-18706600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:18705800-18706600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:18705800-18706800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr19:18705800-18706800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr19:18705800-18706800	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr19:18705800-18707200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:18705800-18707800	Enhancers	K562	blood
21	chr19:18705800-18708000	Enhancers	Right Ventricle	heart
22	chr19:18705800-18714200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:18706000-18706600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr19:18706000-18706600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr19:18706000-18706600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr19:18706000-18706600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:18706000-18706600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr19:18706000-18706600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:18706000-18706600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:18706000-18706800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
31	chr19:18706000-18706800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:18706000-18706800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
33	chr19:18706000-18707200	Weak transcription	Pancreas	Pancrea
34	chr19:18706000-18707400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:18706000-18707400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr19:18706000-18707400	Weak transcription	Left Ventricle	heart
37	chr19:18706000-18709400	Weak transcription	Esophagus	oesophagus
38	chr19:18706000-18712600	Weak transcription	HSMM	muscle
39	chr19:18706000-18713600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr19:18706000-18714000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:18706200-18706600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:18706200-18706600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:18706200-18706600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
44	chr19:18706200-18706800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr19:18706200-18707000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr19:18706200-18707400	Weak transcription	Ovary	ovary
47	chr19:18706200-18707400	Strong transcription	HepG2	liver
48	chr19:18706200-18708200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:18706200-18714400	Weak transcription	Right Atrium	heart
50	chr19:18706400-18706600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links