Variant report

Variant	rs11083567
Chromosome Location	chr19:41318306-41318307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41312066-41318528	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41309752-41318497	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:41307117-41318353	K562	blood:	n/a	n/a
4	CTCF	chr19:41318022-41318367	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:41318003-41318330	GM12878	blood:	n/a	n/a
6	CTCF	chr19:41318200-41318350	HRPEpiC	eye:	n/a	n/a
7	POLR2A	chr19:41317690-41318319	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr19:41318103-41318315	Spleen_OC	spleen:	n/a	n/a
9	POLR2A	chr19:41316307-41318345	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:41317837-41318318	A549	lung:	n/a	n/a
11	CTCF	chr19:41318005-41318384	K562	blood:	n/a	n/a
12	POLR2A	chr19:41318101-41318442	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr19:41317499-41318389	GM12891	blood:	n/a	n/a
14	CTCF	chr19:41318180-41318330	GM12878	blood:	n/a	n/a
15	STAT3	chr19:41318253-41318433	MCF10A-Er-Src	breast:	n/a	n/a
16	SPI1	chr19:41318223-41318654	HL-60	blood:	n/a	n/a
17	POLR2A	chr19:41317692-41318359	GM12878	blood:	n/a	n/a
18	BCL3	chr19:41317727-41318420	A549	lung:	n/a	n/a
19	POLR2A	chr19:41317313-41318443	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41312625..41314191-chr19:41317244..41319686,2	MCF-7	breast:
2	chr19:41304267..41305951-chr19:41317494..41319797,2	MCF-7	breast:

No data

Variant related genes	Relation type
CYP2T2P	TF binding region
ENSG00000269858	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10403040	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10405596	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10411008	0.82[ASN][1000 genomes]
rs10413760	0.82[ASN][1000 genomes]
rs10416308	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10423139	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11083568	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881124	0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17713068	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs2233152	0.82[CHD][hapmap]
rs2287691	0.85[JPT][hapmap]
rs2287692	0.82[CHD][hapmap]
rs28660501	0.84[ASN][1000 genomes]
rs3745213	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs8113056	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11083567	STRN4	cis	cerebellum	SCAN
rs11083567	ZNF230	cis	cerebellum	SCAN
rs11083567	PPFIA3	cis	cerebellum	SCAN
rs11083567	ZNF114	cis	parietal	SCAN
rs11083567	GPR77	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41315000-41324400	Weak transcription	HepG2	liver
2	chr19:41315000-41332600	Weak transcription	Aorta	Aorta
3	chr19:41315800-41318400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:41316000-41319400	Enhancers	Spleen	Spleen
5	chr19:41316000-41319800	Enhancers	Fetal Heart	heart
6	chr19:41316200-41318400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:41316200-41318400	Active TSS	Brain Angular Gyrus	brain
8	chr19:41316200-41324400	Weak transcription	Gastric	stomach
9	chr19:41316400-41318400	Active TSS	Primary T cells from cord blood	blood
10	chr19:41316400-41318800	Weak transcription	HSMMtube	muscle
11	chr19:41316400-41325400	Weak transcription	Dnd41	blood
12	chr19:41316600-41318400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr19:41317000-41318800	Weak transcription	HSMM	muscle
14	chr19:41317200-41318400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:41317200-41318400	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr19:41317200-41318400	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr19:41317200-41318400	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr19:41317200-41318400	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr19:41317200-41318600	Enhancers	NH-A	brain
20	chr19:41317200-41319200	Enhancers	Lung	lung
21	chr19:41317200-41320800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr19:41317400-41318400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:41317400-41318400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:41317400-41318400	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr19:41317400-41318400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:41317400-41318400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr19:41317400-41318400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:41317400-41318400	Flanking Active TSS	Fetal Lung	lung
29	chr19:41317400-41318400	Bivalent Enhancer	GM12878-XiMat	blood
30	chr19:41317400-41318800	Weak transcription	NHLF	lung
31	chr19:41317400-41319800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:41317400-41320200	Enhancers	Placenta	Placenta
33	chr19:41317400-41320400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr19:41317600-41318400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
35	chr19:41317600-41318400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:41317600-41318400	Active TSS	Brain Cingulate Gyrus	brain
37	chr19:41317600-41318600	Enhancers	K562	blood
38	chr19:41317600-41318800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:41317600-41318800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr19:41317600-41318800	Weak transcription	HMEC	breast
41	chr19:41317600-41320400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:41317600-41324000	Weak transcription	Hela-S3	cervix
43	chr19:41317600-41324400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:41317800-41318400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:41317800-41318800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:41317800-41319200	Enhancers	Adipose Nuclei	Adipose
47	chr19:41317800-41319400	Enhancers	Colonic Mucosa	Colon
48	chr19:41317800-41320000	Enhancers	Brain Substantia Nigra	brain
49	chr19:41317800-41324200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:41317800-41324400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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