Variant report

Variant	rs4802030
Chromosome Location	chr19:39957030-39957031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39956671-39957116	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39956888-39957108	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39956555-39957707	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:39956994-39957162	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:39956854-39957254	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:39956742-39957362	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:39956668-39957147	GM12891	blood:	n/a	n/a
9	MYC	chr19:39956962-39957030	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:39948878..39954067-chr19:39954959..39958425,6	K562	blood:
2	chr19:39955020..39957486-chr19:39970318..39972255,2	MCF-7	breast:
3	chr19:39956900..39963294-chr19:39968062..39973681,7	MCF-7	breast:
4	chr19:39956852..39958714-chr19:39959801..39965417,6	K562	blood:

No data

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000196235	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10420073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423161	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10423921	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10425652	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10426543	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882744	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1529733	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1865094	0.85[GIH][hapmap]
rs3786950	0.86[CHB][hapmap]
rs45568533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802033	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs4803238	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs4803241	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4803244	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59269050	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61480418	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62120691	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7245986	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246329	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73035459	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73035461	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106642	0.84[ASN][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	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4802030	PRKD2	cis	cerebellum	SCAN
rs4802030	B3GNT8	cis	parietal	SCAN
rs4802030	CD177	cis	parietal	SCAN
rs4802030	RPS16	cis	lymphoblastoid	seeQTL
rs4802030	NUMBL	cis	parietal	SCAN
rs4802030	POU2F2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
3	chr19:39938600-39967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:39939200-39967600	Strong transcription	Fetal Thymus	thymus
5	chr19:39939400-39968800	Strong transcription	Fetal Stomach	stomach
6	chr19:39940000-39968000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr19:39940200-39968600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:39940200-39968600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:39940200-39968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:39940200-39970600	Weak transcription	Fetal Heart	heart
11	chr19:39941400-39967400	Strong transcription	Fetal Intestine Large	intestine
12	chr19:39942000-39967400	Strong transcription	Thymus	Thymus
13	chr19:39942000-39967600	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:39942200-39967600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr19:39942200-39967600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:39942200-39967600	Strong transcription	Placenta	Placenta
17	chr19:39942200-39967600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr19:39942200-39967800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr19:39942600-39967600	Strong transcription	Liver	Liver
20	chr19:39942800-39967400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:39942800-39967800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39943000-39967200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr19:39943000-39967800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:39943200-39967800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:39943400-39967400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:39944000-39967400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:39945800-39966200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:39946600-39967600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:39946600-39967600	Strong transcription	Primary B cells from cord blood	blood
30	chr19:39946600-39967800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:39946800-39967800	Strong transcription	Osteobl	bone
32	chr19:39947000-39967800	Strong transcription	Primary T cells from cord blood	blood
33	chr19:39947200-39968800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:39947400-39961200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:39947400-39965000	Strong transcription	Lung	lung
36	chr19:39947400-39967600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:39947400-39967600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:39947400-39967600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:39947400-39967600	Strong transcription	Adipose Nuclei	Adipose
40	chr19:39947400-39967800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:39947400-39968000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:39947400-39968000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:39947400-39968000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr19:39947800-39968000	Strong transcription	NHEK	skin
45	chr19:39948800-39967800	Strong transcription	HSMM	muscle
46	chr19:39949800-39960800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr19:39953600-39967800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr19:39954000-39961200	Strong transcription	NH-A	brain
49	chr19:39954000-39963200	Strong transcription	HUVEC	blood vessel
50	chr19:39954000-39967200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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