Variant report

Variant	rs10491176
Chromosome Location	chr17:66539435-66539436
allele	C/T
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	POLR2A	chr17:66535303-66540040	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:66534614-66539539	GM12878	blood:	n/a	n/a
3	STAT3	chr17:66539171-66539528	MCF10A-Er-Src	breast:	n/a	chr17:66539334-66539345
4	FOXA2	chr17:66539120-66539563	A549	lung:	n/a	n/a
5	SP1	chr17:66539118-66539590	A549	lung:	n/a	n/a
6	FOXA2	chr17:66539132-66539695	A549	lung:	n/a	n/a
7	POLR2A	chr17:66539118-66539517	HepG2	liver:	n/a	n/a
8	FOS	chr17:66539134-66539490	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr17:66539134-66539537	MCF10A-Er-Src	breast:	n/a	chr17:66539334-66539345
10	STAT3	chr17:66539170-66539521	MCF10A-Er-Src	breast:	n/a	chr17:66539334-66539345
11	FOS	chr17:66539170-66539443	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr17:66537968-66539466	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:66528378-66541028	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66509250..66511874-chr17:66538190..66540879,2	MCF-7	breast:

Variant related genes	Relation type
FAM20A	TF binding region
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10468444	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10852738	1.00[CEU][hapmap]
rs16972996	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];1.00[EUR][1000 genomes]
rs16973034	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2015212	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302235	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3785905	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55736761	1.00[EUR][1000 genomes]
rs7221724	1.00[EUR][1000 genomes]
rs72847782	0.99[EUR][1000 genomes]
rs72847784	0.99[EUR][1000 genomes]
rs72847785	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847787	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847789	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847790	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72847794	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847801	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74000753	1.00[EUR][1000 genomes]
rs8072598	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8082254	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv510723	chr17:66529668-66557425	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv522126	chr17:66538239-66548457	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10491176	PITPNC1	cis	cerebellum	SCAN
rs10491176	AMZ2P1	cis	parietal	SCAN
rs10491176	WIPI1	cis	cerebellum	SCAN
rs10491176	PRKAR1A	cis	multi-tissue	Pritchard
rs10491176	WIPI1	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66520400-66539800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:66523200-66542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:66526600-66539800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr17:66526800-66540600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:66527600-66554200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:66531200-66552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:66531400-66540000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:66531800-66540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr17:66532400-66540200	Strong transcription	Osteobl	bone
10	chr17:66532800-66539600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:66533000-66555200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:66533800-66545400	Weak transcription	Psoas Muscle	Psoas
13	chr17:66533800-66549800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr17:66534000-66541400	Weak transcription	Colon Smooth Muscle	Colon
15	chr17:66534000-66541800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr17:66534000-66552800	Weak transcription	Fetal Kidney	kidney
17	chr17:66534200-66563200	Weak transcription	Ovary	ovary
18	chr17:66534600-66539800	Weak transcription	Primary B cells from cord blood	blood
19	chr17:66534800-66554200	Weak transcription	NHDF-Ad	bronchial
20	chr17:66535000-66540000	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr17:66535200-66542800	Weak transcription	Fetal Brain Female	brain
22	chr17:66535400-66540200	Genic enhancers	Liver	Liver
23	chr17:66536200-66540200	Weak transcription	Right Atrium	heart
24	chr17:66536400-66540000	Strong transcription	Fetal Muscle Leg	muscle
25	chr17:66536400-66541400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:66536600-66539800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr17:66536600-66542600	Weak transcription	Pancreas	Pancrea
28	chr17:66536800-66539800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr17:66536800-66539800	Weak transcription	Fetal Thymus	thymus
30	chr17:66536800-66540200	Weak transcription	Fetal Lung	lung
31	chr17:66536800-66540200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr17:66536800-66540200	Weak transcription	HSMMtube	muscle
33	chr17:66536800-66540800	Weak transcription	Fetal Heart	heart
34	chr17:66537000-66539800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:66537000-66540200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:66537000-66540200	Strong transcription	Placenta	Placenta
37	chr17:66537000-66543800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr17:66537000-66544400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:66537200-66540200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr17:66537200-66550600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr17:66537200-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr17:66537400-66539800	Weak transcription	Fetal Intestine Small	intestine
43	chr17:66537400-66541400	Weak transcription	NHLF	lung
44	chr17:66537400-66548000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:66537400-66551800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:66537600-66539800	Weak transcription	Esophagus	oesophagus
47	chr17:66537600-66543000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr17:66537600-66543600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr17:66537600-66545400	Weak transcription	Primary T cells from cord blood	blood
50	chr17:66537800-66539800	Weak transcription	Gastric	stomach

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