Variant report

Variant	rs10235680
Chromosome Location	chr7:26908596-26908597
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	MXI1	chr7:26908549-26908971	Hela-S3	cervix:	n/a	n/a
2	SP1	chr7:26908375-26909029	HCT-116	colon:	n/a	n/a
3	FOS	chr7:26908200-26909096	MCF10A-Er-Src	breast:	n/a	chr7:26908619-26908626 chr7:26908458-26908472 chr7:26908618-26908626 chr7:26908614-26908625 chr7:26908618-26908627
4	CHD2	chr7:26908463-26908759	Hela-S3	cervix:	n/a	n/a
5	E2F4	chr7:26908254-26908988	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr7:26908596-26908906	MCF10A-Er-Src	breast:	n/a	chr7:26908617-26908626 chr7:26908618-26908627
7	JUND	chr7:26908438-26909117	Hela-S3	cervix:	n/a	chr7:26908619-26908626 chr7:26908458-26908472 chr7:26908618-26908626 chr7:26908614-26908625 chr7:26908618-26908627
8	FOSL1	chr7:26908383-26909058	HCT-116	colon:	n/a	chr7:26908619-26908626 chr7:26908458-26908472 chr7:26908618-26908626 chr7:26908614-26908625 chr7:26908618-26908627
9	RCOR1	chr7:26908543-26909146	Hela-S3	cervix:	n/a	n/a
10	GTF2F1	chr7:26908521-26908986	Hela-S3	cervix:	n/a	n/a
11	MAX	chr7:26908507-26908927	Hela-S3	cervix:	n/a	chr7:26908634-26908644 chr7:26908617-26908626 chr7:26908618-26908627
12	FOS	chr7:26908208-26909095	MCF10A-Er-Src	breast:	n/a	chr7:26908619-26908626 chr7:26908458-26908472 chr7:26908618-26908626 chr7:26908614-26908625 chr7:26908618-26908627
13	SMC3	chr7:26908485-26908936	Hela-S3	cervix:	n/a	n/a
14	FOS	chr7:26908480-26909112	MCF10A-Er-Src	breast:	n/a	chr7:26908619-26908626 chr7:26908618-26908626 chr7:26908614-26908625 chr7:26908618-26908627
15	JUND	chr7:26908406-26909084	HCT-116	colon:	n/a	chr7:26908619-26908626 chr7:26908458-26908472 chr7:26908618-26908626 chr7:26908614-26908625 chr7:26908618-26908627
16	RFX5	chr7:26908382-26909057	Hela-S3	cervix:	n/a	n/a
17	MYC	chr7:26908488-26909083	MCF10A-Er-Src	breast:	n/a	chr7:26908634-26908644 chr7:26908617-26908626 chr7:26908618-26908627
18	CEBPB	chr7:26908280-26909348	Hela-S3	cervix:	n/a	chr7:26909194-26909205
19	FOS	chr7:26908473-26909102	MCF10A-Er-Src	breast:	n/a	chr7:26908619-26908626 chr7:26908618-26908626 chr7:26908614-26908625 chr7:26908618-26908627
20	EP300	chr7:26908487-26909156	Hela-S3	cervix:	n/a	chr7:26908618-26908627 chr7:26908617-26908626
21	POLR2A	chr7:26908531-26908810	MCF10A-Er-Src	breast:	n/a	n/a
22	MYC	chr7:26908489-26908958	MCF10A-Er-Src	breast:	n/a	chr7:26908634-26908644 chr7:26908617-26908626 chr7:26908618-26908627
23	MAFK	chr7:26908544-26908986	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:26902484..26906060-chr7:26906980..26911277,7	MCF-7	breast:
2	chr7:26904576..26906244-chr7:26908580..26910175,2	K562	blood:
3	chr7:26903581..26905887-chr7:26906835..26909614,2	MCF-7	breast:

Variant related genes	Relation type
SKAP2	TF binding region
ENSG00000005020	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10085562	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10227575	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10231080	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10231272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10238067	0.85[EUR][1000 genomes]
rs10244462	0.85[CEU][hapmap]
rs10246300	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10246483	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10246578	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10247117	0.88[EUR][1000 genomes]
rs10248232	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10249383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250097	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10250304	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10250321	0.85[EUR][1000 genomes]
rs10251817	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10252268	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254460	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10254467	1.00[JPT][hapmap]
rs10257057	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10261927	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10262212	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10262527	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10262797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265607	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10271306	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277060	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10280403	0.88[EUR][1000 genomes]
rs1030647	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10486473	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10486474	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs10486480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486481	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155150	0.81[EUR][1000 genomes]
rs12333690	0.88[EUR][1000 genomes]
rs12334154	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1391805	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs1548482	0.82[CEU][hapmap]
rs17154428	1.00[JPT][hapmap]
rs17154538	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17310268	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17310851	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs17310907	0.85[CEU][hapmap]
rs17313134	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17323962	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370293	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17371905	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs213524	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs28465643	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28781274	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3735547	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs3801835	1.00[JPT][hapmap]
rs4141345	1.00[JPT][hapmap]
rs4141346	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs586947	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs67719086	0.88[EUR][1000 genomes]
rs6950668	1.00[JPT][hapmap]
rs6954621	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6960091	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73069515	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069545	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7779269	0.85[EUR][1000 genomes]
rs7782851	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7783807	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs7784380	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs7786308	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7786456	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7806174	0.85[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26905200-26908600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:26908000-26908600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:26908000-26908800	Enhancers	Hela-S3	cervix
4	chr7:26908000-26909400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:26908000-26909400	Enhancers	HMEC	breast
6	chr7:26908000-26909400	Enhancers	NHEK	skin
7	chr7:26908200-26908600	Flanking Active TSS	HSMMtube	muscle
8	chr7:26908200-26908800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:26908200-26908800	Enhancers	NHDF-Ad	bronchial
10	chr7:26908200-26909200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr7:26908200-26909200	Enhancers	HSMM	muscle
12	chr7:26908400-26908800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:26908400-26908800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:26908400-26908800	Enhancers	Osteobl	bone
15	chr7:26908400-26909000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:26908400-26909000	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links