Variant report

Variant	rs741706
Chromosome Location	chr19:19281672-19281673
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr19:19280916-19281701	K562	blood:	n/a	chr19:19281264-19281273
2	POLR2A	chr19:19281607-19281687	MCF10A-Er-Src	breast:	n/a	n/a
3	ZBTB7A	chr19:19280725-19281937	ECC-1	luminal epithelium:	n/a	chr19:19281264-19281273
4	POLR2A	chr19:19280288-19281744	Raji	blood:	n/a	n/a
5	POLR2A	chr19:19281547-19281847	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:19281558-19281729	GM12878	blood:	n/a	n/a
7	ELF1	chr19:19280640-19281865	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:19281567-19281731	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:19254048..19257177-chr19:19281420..19283386,3	K562	blood:
2	chr19:19280644..19282541-chr19:19431552..19433735,2	MCF-7	breast:
3	chr19:19171096..19173278-chr19:19281615..19284130,2	K562	blood:
4	chr19:19281578..19283666-chr19:19326802..19329714,2	K562	blood:
5	chr19:19280114..19282646-chr19:19429552..19431405,2	MCF-7	breast:
6	chr19:19256287..19258012-chr19:19281605..19284547,2	MCF-7	breast:
7	chr19:19279506..19282646-chr19:19302669..19304636,3	MCF-7	breast:
8	chr19:19276770..19279555-chr19:19281152..19284239,3	K562	blood:

No data

Variant related genes	Relation type
MEF2B	TF binding region
ENSG00000105705	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000129933	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1005980	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10417796	0.84[EUR][1000 genomes]
rs10418053	0.96[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs1050544	0.96[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs10854008	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10854009	0.83[EUR][1000 genomes]
rs10854012	0.88[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11669408	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669860	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669861	0.88[EUR][1000 genomes]
rs12609573	1.00[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12972894	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12974672	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975096	0.81[EUR][1000 genomes]
rs12975253	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975290	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980269	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980955	0.85[EUR][1000 genomes]
rs12981160	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1858846	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238668	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239369	0.88[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239370	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2283623	0.85[EUR][1000 genomes]
rs2314035	0.84[EUR][1000 genomes]
rs35342977	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787040	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808185	0.82[EUR][1000 genomes]
rs539	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62135499	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71332145	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250650	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256811	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72997174	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759999	0.80[EUR][1000 genomes]
rs8101388	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs741706	ZNF682	cis	parietal	SCAN
rs741706	RAB8A	cis	parietal	SCAN
rs741706	PDE4C	cis	cerebellum	SCAN
rs741706	C19orf50	cis	cerebellum	SCAN
rs741706	C19orf50	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19249600-19282600	Weak transcription	NHLF	lung
2	chr19:19259000-19290200	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:19268200-19282600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:19268800-19287200	Weak transcription	Dnd41	blood
5	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
6	chr19:19280200-19281800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:19280200-19281800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr19:19280400-19281800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:19280400-19281800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:19280400-19281800	Enhancers	Stomach Mucosa	stomach
11	chr19:19280400-19281800	Flanking Active TSS	HepG2	liver
12	chr19:19280600-19281800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr19:19280600-19282000	Bivalent Enhancer	Fetal Stomach	stomach
14	chr19:19280800-19281800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:19280800-19282000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:19280800-19282000	Enhancers	Fetal Heart	heart
17	chr19:19280800-19287000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:19280800-19301600	Weak transcription	NHEK	skin
19	chr19:19281000-19281800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr19:19281000-19281800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:19281000-19281800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr19:19281000-19281800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:19281000-19281800	Enhancers	Fetal Thymus	thymus
24	chr19:19281000-19282200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr19:19281000-19283400	Enhancers	Placenta	Placenta
26	chr19:19281000-19287000	Weak transcription	Primary T cells from cord blood	blood
27	chr19:19281200-19281800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:19281200-19281800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr19:19281200-19281800	Enhancers	Left Ventricle	heart
30	chr19:19281200-19281800	Enhancers	Pancreas	Pancrea
31	chr19:19281200-19281800	Enhancers	Spleen	Spleen
32	chr19:19281200-19282000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr19:19281200-19282600	Weak transcription	Psoas Muscle	Psoas
34	chr19:19281200-19282800	Weak transcription	Liver	Liver
35	chr19:19281200-19282800	Weak transcription	HSMM	muscle
36	chr19:19281200-19283000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:19281200-19283800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:19281200-19283800	Enhancers	GM12878-XiMat	blood
39	chr19:19281200-19287400	Weak transcription	Aorta	Aorta
40	chr19:19281400-19281800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr19:19281400-19281800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:19281400-19281800	Enhancers	Brain Anterior Caudate	brain
43	chr19:19281400-19281800	Enhancers	Brain Hippocampus Middle	brain
44	chr19:19281400-19281800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:19281400-19281800	Enhancers	Colonic Mucosa	Colon
46	chr19:19281400-19281800	Enhancers	Ovary	ovary
47	chr19:19281400-19282000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:19281400-19282400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:19281400-19282600	Weak transcription	HSMMtube	muscle
50	chr19:19281400-19282800	Weak transcription	Muscle Satellite Cultured Cells	--

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