Variant report

Variant	rs17432580
Chromosome Location	chr2:63167051-63167052
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	FOSL2	chr2:63166788-63167384	SK-N-SH	brain:	n/a	chr2:63167018-63167026 chr2:63167016-63167028
2	FOS	chr2:63166779-63167286	MCF10A-Er-Src	breast:	n/a	chr2:63167018-63167026 chr2:63167016-63167028
3	MAFK	chr2:63166981-63167702	IMR90	lung:	n/a	chr2:63167422-63167436 chr2:63167419-63167435
4	NFIC	chr2:63166882-63167191	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:63166685-63168660	HepG2	liver:	n/a	n/a
6	FOS	chr2:63166923-63167266	MCF10A-Er-Src	breast:	n/a	chr2:63167018-63167026 chr2:63167016-63167028
7	JUND	chr2:63166851-63167245	SK-N-SH	brain:	n/a	chr2:63167018-63167026 chr2:63167016-63167028
8	MYC	chr2:63166854-63167189	MCF10A-Er-Src	breast:	n/a	chr2:63167018-63167027
9	STAT3	chr2:63166996-63167188	MCF10A-Er-Src	breast:	n/a	n/a
10	RCOR1	chr2:63166631-63167320	IMR90	lung:	n/a	n/a
11	MAFF	chr2:63167050-63167606	HepG2	liver:	n/a	chr2:63167418-63167436
12	CEBPB	chr2:63166747-63167138	IMR90	lung:	n/a	n/a
13	FOS	chr2:63166844-63167259	MCF10A-Er-Src	breast:	n/a	chr2:63167018-63167026 chr2:63167016-63167028
14	MYC	chr2:63166973-63167151	MCF10A-Er-Src	breast:	n/a	chr2:63167018-63167027
15	FOS	chr2:63166925-63167251	MCF10A-Er-Src	breast:	n/a	chr2:63167018-63167026 chr2:63167016-63167028
16	TCF12	chr2:63166770-63167389	SK-N-SH	brain:	n/a	n/a
17	STAT3	chr2:63166746-63167146	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr2:63166892-63167226	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr2:63166853-63167400	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63164960..63167848-chr2:63174412..63177357,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTX1-4	chr2:63167051-63167417	NONHSAT071040

Variant related genes	Relation type
ENSG00000237162	TF binding region
EHBP1	TF binding region
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12612046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613453	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12614162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17432559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs17432615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17473084	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17598689	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598881	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657533	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877027	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17432580	TMEM17	cis	cerebellum	SCAN
rs17432580	PEX13	cis	cerebellum	SCAN
rs17432580	OTX1	cis	Whole Blood	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63142400-63190800	Weak transcription	Brain Angular Gyrus	brain
2	chr2:63150600-63176000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:63151200-63167200	Weak transcription	HSMM	muscle
4	chr2:63151200-63171200	Weak transcription	Ovary	ovary
5	chr2:63151200-63175600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:63151200-63182800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:63151400-63169600	Weak transcription	A549	lung
8	chr2:63151400-63171400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:63151400-63194200	Weak transcription	Esophagus	oesophagus
10	chr2:63151400-63194200	Weak transcription	Fetal Brain Male	brain
11	chr2:63151400-63200800	Weak transcription	Fetal Stomach	stomach
12	chr2:63151400-63208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:63152200-63169200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:63152200-63175600	Weak transcription	Primary T cells from cord blood	blood
16	chr2:63154400-63209000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:63155400-63209000	Weak transcription	Psoas Muscle	Psoas
18	chr2:63157400-63175600	Weak transcription	Left Ventricle	heart
19	chr2:63157400-63188800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:63157400-63207400	Weak transcription	Pancreas	Pancrea
21	chr2:63160200-63190000	Weak transcription	Primary B cells from cord blood	blood
22	chr2:63161800-63171200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:63161800-63184400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:63162000-63196800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:63162000-63199800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:63163000-63170800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:63163200-63167200	Weak transcription	NHLF	lung
28	chr2:63163600-63167800	Strong transcription	HepG2	liver
29	chr2:63164800-63167200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:63164800-63167400	Enhancers	NH-A	brain
31	chr2:63165000-63167600	Enhancers	HSMMtube	muscle
32	chr2:63165000-63171600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:63165200-63209200	Weak transcription	Aorta	Aorta
34	chr2:63165800-63167200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:63166000-63167400	Strong transcription	Liver	Liver
36	chr2:63166200-63167800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:63166600-63167600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:63166600-63167600	Enhancers	HMEC	breast
39	chr2:63166800-63167200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:63166800-63167400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:63166800-63167400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:63166800-63167400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:63166800-63167800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr2:63166800-63167800	Enhancers	NHDF-Ad	bronchial
45	chr2:63166800-63167800	Enhancers	NHEK	skin
46	chr2:63166800-63167800	Enhancers	Osteobl	bone
47	chr2:63167000-63194000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links