Variant report

Variant	rs12537656
Chromosome Location	chr7:47693951-47693952
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	GATA3	chr7:47693159-47694175	SK-N-SH	brain:	n/a	chr7:47693808-47693817 chr7:47693264-47693276 chr7:47693266-47693273 chr7:47693266-47693273 chr7:47693265-47693275 chr7:47693266-47693273
2	GATA3	chr7:47693032-47694204	A549	lung:	n/a	chr7:47693808-47693817 chr7:47693264-47693276 chr7:47693266-47693273 chr7:47693266-47693273 chr7:47693265-47693275 chr7:47693266-47693273
3	SP1	chr7:47693161-47694017	A549	lung:	n/a	n/a
4	MAX	chr7:47693388-47694023	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr7:47693316-47694464	A549	lung:	n/a	n/a
6	FOS	chr7:47693702-47693965	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr7:47693139-47694119	SK-N-SH	brain:	n/a	n/a
8	GTF3C2	chr7:47693602-47694167	Hela-S3	cervix:	n/a	n/a
9	PBX3	chr7:47693267-47694122	SK-N-SH	brain:	n/a	n/a
10	FOS	chr7:47693693-47694002	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr7:47693215-47694023	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr7:47693204-47694190	SK-N-SH	brain:	n/a	chr7:47693808-47693817 chr7:47693264-47693276 chr7:47693266-47693273 chr7:47693266-47693273 chr7:47693265-47693275 chr7:47693266-47693273
13	MAX	chr7:47693083-47694077	A549	lung:	n/a	chr7:47693338-47693347
14	RPC155	chr7:47693546-47694439	Hela-S3	cervix:	n/a	n/a
15	RCOR1	chr7:47693272-47694660	IMR90	lung:	n/a	n/a
16	FOS	chr7:47693693-47694009	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA2	chr7:47693298-47694185	HUVEC	blood vessel:	n/a	chr7:47693808-47693817
18	FOS	chr7:47693642-47694009	HUVEC	blood vessel:	n/a	n/a
19	TCF12	chr7:47693001-47694136	A549	lung:	n/a	n/a
20	TCF12	chr7:47693175-47694101	SK-N-SH	brain:	n/a	n/a
21	MAX	chr7:47692342-47694097	A549	lung:	n/a	chr7:47693338-47693347
22	NFIC	chr7:47693117-47694080	SK-N-SH	brain:	n/a	chr7:47693556-47693572

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:47693946-47693996	NH-A	brain:	n/a
2	chr7:47693946-47693996	AoSMC	blood vessel:	n/a
3	chr7:47693946-47693996	PFSK-1	brain:	n/a
4	chr7:47693946-47693996	MCF-7	breast:	n/a
5	chr7:47693946-47693996	HRPEpiC	eye:	n/a
6	chr7:47693946-47693996	CMK	blood:	n/a
7	chr7:47693946-47693996	U87	brain:	n/a
8	chr7:47693946-47693996	HRCEpiC	kidney:	n/a
9	chr7:47693946-47693996	IMR90	lung:	fetal
10	chr7:47693946-47693996	NHDF-neo	bronchial:	n/a
11	chr7:47693946-47693996	AG09309	skin:	n/a
12	chr7:47693946-47693996	PrEC	prostate:	n/a
13	chr7:47693946-47693996	HCT-116	colon:	n/a
14	chr7:47693946-47693996	SK-N-SH	brain:	n/a
15	chr7:47693946-47693996	Jurkat	blood:	n/a
16	chr7:47693946-47693996	HCPEpiC	choroid plexus:	n/a
17	chr7:47693946-47693996	GM12892	blood:	n/a
18	chr7:47693946-47693996	SK-N-MC	brain:	n/a
19	chr7:47693946-47693996	HAEpiC	amniotic membrane:	n/a
20	chr7:47693946-47693996	NB4	blood:	n/a
21	chr7:47693946-47693996	HCM	heart:	n/a
22	chr7:47693946-47693996	ECC-1	luminal epithelium:	n/a
23	chr7:47693946-47693996	GM12891	blood:	n/a
24	chr7:47693946-47693996	Hela-S3	cervix:	n/a
25	chr7:47693946-47693996	T-47D	breast:	n/a
26	chr7:47693946-47693996	HMEC	breast:	n/a
27	chr7:47693946-47693996	H1-hESC	embryonic stem cell:	embryo
28	chr7:47693946-47693996	AG10803	skin:	n/a
29	chr7:47693946-47693996	HL-60	blood:	n/a
30	chr7:47693946-47693996	SKMC	muscle:	n/a
31	chr7:47693946-47693996	BE2_C	brain:	n/a
32	chr7:47693946-47693996	HCF	heart:	n/a
33	chr7:47693946-47693996	HepG2	liver:	n/a
34	chr7:47693946-47693996	SK-N-SH_RA	brain:	n/a
35	chr7:47693946-47693996	SAEC	small airway:	n/a
36	chr7:47693946-47693996	BJ	skin:	n/a
37	chr7:47693946-47693996	HRE	kidney:	n/a
38	chr7:47693946-47693996	GM12878	blood:	n/a
39	chr7:47693946-47693996	HUVEC	blood vessel:	n/a
40	chr7:47693946-47693996	Caco-2	colon:	n/a
41	chr7:47693946-47693996	GM19239	blood:	n/a
42	chr7:47693946-47693996	LNCaP	prostate:	n/a
43	chr7:47693946-47693996	PANC-1	pancreas:	n/a
44	chr7:47693946-47693996	K562	blood:	n/a
45	chr7:47693946-47693996	ProgFib	skin:	n/a
46	chr7:47693946-47693996	HNPCEpiC	eye:	n/a
47	chr7:47693946-47693996	HIPEpiC	eye:	n/a
48	chr7:47693946-47693996	A549	lung:	n/a
49	chr7:47693946-47693996	AG04450	lung:	fetal
50	chr7:47693946-47693996	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47691927..47694720-chr7:47708904..47710828,2	MCF-7	breast:

Variant related genes	Relation type
C7orf65	TF binding region
C7orf65	CpG island

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10951916	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11766347	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11768009	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11770543	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs12531737	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12535121	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12535169	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13242997	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13243511	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4724606	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4724607	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4724608	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4724610	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6969715	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7790431	0.83[ASN][1000 genomes]
rs7790476	0.80[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs965924	1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12537656	CDC14C	cis	parietal	SCAN
rs12537656	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47687200-47695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:47688800-47694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:47689000-47694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:47689800-47694800	Enhancers	NH-A	brain
5	chr7:47690000-47695000	Enhancers	NHDF-Ad	bronchial
6	chr7:47690400-47694800	Enhancers	NHLF	lung
7	chr7:47690600-47695600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:47691600-47694400	Weak transcription	Adipose Nuclei	Adipose
9	chr7:47692200-47694600	Enhancers	HSMMtube	muscle
10	chr7:47692600-47694800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:47693000-47694600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:47693000-47694800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:47693200-47694200	Enhancers	Lung	lung
14	chr7:47693200-47694200	Enhancers	Spleen	Spleen
15	chr7:47693200-47694200	Enhancers	HUVEC	blood vessel
16	chr7:47693200-47694800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:47693200-47695000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:47693200-47695000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr7:47693200-47695200	Enhancers	Fetal Muscle Leg	muscle
20	chr7:47693200-47695400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr7:47693200-47695400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr7:47693200-47695400	Enhancers	Placenta	Placenta
23	chr7:47693400-47694000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:47693400-47694400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr7:47693400-47694600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr7:47693400-47694800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr7:47693400-47694800	Enhancers	Fetal Muscle Trunk	muscle
28	chr7:47693400-47694800	Enhancers	HMEC	breast
29	chr7:47693400-47695000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:47693400-47695000	Enhancers	HSMM	muscle
31	chr7:47693400-47695400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:47693600-47694000	Enhancers	NHEK	skin
33	chr7:47693600-47694600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:47693600-47695000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr7:47693600-47695000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:47693600-47695200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr7:47693800-47694200	Enhancers	Osteobl	bone
38	chr7:47693800-47694600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:47693800-47694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:47693800-47694600	Enhancers	Hela-S3	cervix
41	chr7:47693800-47695200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr7:47693800-47695400	Enhancers	A549	lung
43	chr7:47693800-47697800	Weak transcription	HepG2	liver

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