Variant report

Variant	rs11783045
Chromosome Location	chr8:11056175-11056176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr8:11055983-11059769	SK-N-SH	brain:	n/a	chr8:11059259-11059271 chr8:11057745-11057758 chr8:11057624-11057637
2	CHD1	chr8:11056014-11056176	H1-hESC	embryonic stem cell:	n/a	n/a
3	STAT3	chr8:11056131-11056404	MCF10A-Er-Src	breast:	n/a	chr8:11056244-11056252
4	POLR2A	chr8:11056002-11059542	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr8:11056045-11056281	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11042275..11044106-chr8:11054861..11057806,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270076	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10087767	1.00[CHB][hapmap]
rs10088853	1.00[CHB][hapmap];0.81[TSI][hapmap]
rs10095003	1.00[ASN][1000 genomes]
rs10100660	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101329	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10110684	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503417	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10903337	1.00[CHB][hapmap]
rs11775489	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11776603	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11777355	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777887	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777918	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778121	1.00[CHB][hapmap]
rs11783890	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785237	1.00[ASN][1000 genomes]
rs11785392	1.00[CHB][hapmap]
rs11989369	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13248014	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13248264	1.00[CHB][hapmap]
rs13248300	1.00[CHB][hapmap]
rs13249916	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13251528	1.00[CHB][hapmap]
rs13256743	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13265553	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs13266785	0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs13273857	1.00[CHB][hapmap]
rs13276708	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13276836	1.00[CHB][hapmap]
rs17152841	1.00[CHB][hapmap]
rs17725480	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17725534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17726209	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17779791	1.00[CHB][hapmap]
rs17782536	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17782554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1987190	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409691	1.00[CHB][hapmap]
rs2409692	1.00[CHB][hapmap]
rs2409693	1.00[CHB][hapmap]
rs2409695	1.00[CHB][hapmap]
rs2409719	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs2409720	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409725	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409726	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409729	1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409730	0.84[ASW][hapmap];0.91[CEU][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3021495	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs3021497	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3021498	1.00[ASN][1000 genomes]
rs3021501	1.00[ASN][1000 genomes]
rs34309263	1.00[ASN][1000 genomes]
rs34367737	1.00[ASN][1000 genomes]
rs35211404	1.00[ASN][1000 genomes]
rs4291231	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4412337	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451268	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618656	1.00[CHB][hapmap]
rs4642600	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4840548	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4841486	1.00[CHB][hapmap]
rs4841497	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4841499	1.00[ASN][1000 genomes]
rs6601561	1.00[CHB][hapmap]
rs6601563	1.00[CHB][hapmap]
rs67418928	1.00[ASN][1000 genomes]
rs67559300	1.00[ASN][1000 genomes]
rs71518512	1.00[ASN][1000 genomes]
rs73198943	1.00[ASN][1000 genomes]
rs7832722	1.00[CHB][hapmap]
rs7844536	0.83[AMR][1000 genomes]
rs9329238	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657544	1.00[CHB][hapmap]

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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11783045	MFHAS1	cis	cerebellum	SCAN
rs11783045	TDH	cis	parietal	SCAN
rs11783045	CLDN23	cis	multi-tissue	Pritchard
rs11783045	MTMR9	cis	parietal	SCAN
rs11783045	FLJ10661	cis	cerebellum	SCAN
rs11783045	C8orf13	cis	multi-tissue	Pritchard
rs11783045	TDH	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11028200-11056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr8:11029600-11056800	Weak transcription	Fetal Intestine Small	intestine
3	chr8:11034600-11057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:11034600-11057000	Weak transcription	Esophagus	oesophagus
5	chr8:11042800-11056600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:11045200-11057000	Weak transcription	Fetal Stomach	stomach
7	chr8:11046400-11056600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr8:11046600-11056600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:11049000-11056800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr8:11050400-11057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:11050600-11056400	Weak transcription	Small Intestine	intestine
12	chr8:11052400-11057000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr8:11053600-11057000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr8:11053800-11056400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr8:11054200-11056200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:11054200-11056400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr8:11054200-11057000	Enhancers	Primary B cells from peripheral blood	blood
18	chr8:11054200-11057200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr8:11054400-11057000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr8:11054600-11056200	Enhancers	HUVEC	blood vessel
21	chr8:11054800-11056200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr8:11054800-11057000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr8:11054800-11059600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:11055000-11056200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:11055000-11056200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr8:11055000-11056400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr8:11055000-11056800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr8:11055000-11057800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr8:11055200-11056200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:11055200-11056200	Weak transcription	Brain Angular Gyrus	brain
31	chr8:11055200-11056200	Weak transcription	Spleen	Spleen
32	chr8:11055200-11056400	Weak transcription	Fetal Kidney	kidney
33	chr8:11055200-11057000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:11055200-11057000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr8:11055400-11056200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr8:11055400-11056200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr8:11055400-11056200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr8:11055400-11056200	Enhancers	NH-A	brain
39	chr8:11055400-11056600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr8:11055400-11056600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:11055400-11056600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr8:11055400-11056800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr8:11055400-11057600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr8:11055400-11059400	Active TSS	GM12878-XiMat	blood
45	chr8:11055600-11056200	Weak transcription	HSMM	muscle
46	chr8:11055600-11056400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr8:11055600-11059400	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr8:11055800-11056200	Enhancers	Brain Germinal Matrix	brain
49	chr8:11055800-11056200	Active TSS	HMEC	breast
50	chr8:11055800-11056600	Weak transcription	Fetal Brain Female	brain

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