Variant report

Variant	rs10259983
Chromosome Location	chr7:26895719-26895720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr7:26895669-26895758	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:26894665..26897647-chr7:27182466..27184718,4	MCF-7	breast:
2	chr7:26892970..26895905-chr7:27178722..27180314,2	MCF-7	breast:
3	chr7:26894828..26897181-chr7:27200837..27202990,2	K562	blood:
4	chr7:26893506..26896293-chr7:26902424..26905026,3	MCF-7	breast:
5	chr7:26894678..26896550-chr7:27170054..27174548,4	MCF-7	breast:

No data

Variant related genes	Relation type
SKAP2	TF binding region
ENSG00000106004	Chromatin interaction
ENSG00000254369	Chromatin interaction
ENSG00000105997	Chromatin interaction
ENSG00000197576	Chromatin interaction
ENSG00000005020	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10215738	0.81[AFR][1000 genomes]
rs10225700	0.84[AFR][1000 genomes]
rs10225924	0.82[AFR][1000 genomes]
rs10227231	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs10227529	0.90[AFR][1000 genomes]
rs10227673	0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs10236221	0.92[AFR][1000 genomes]
rs10242572	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs10244986	0.84[AFR][1000 genomes]
rs10248500	0.86[AFR][1000 genomes]
rs10249931	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10251839	0.92[AFR][1000 genomes]
rs10252275	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10256250	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs10267950	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs10270187	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10272190	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs10272303	0.82[AFR][1000 genomes]
rs10272457	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs10272603	0.92[AFR][1000 genomes]
rs10275896	0.81[AFR][1000 genomes]
rs10276471	0.82[YRI][hapmap]
rs10280476	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10281933	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10486483	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs10486484	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10486485	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs12532199	0.83[AFR][1000 genomes]
rs12532395	0.82[AFR][1000 genomes]
rs12534899	0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs12534921	0.87[AFR][1000 genomes]
rs12535784	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs12536145	0.90[AFR][1000 genomes]
rs12536560	0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs12537323	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs12540045	0.86[AFR][1000 genomes]
rs12540508	0.89[AFR][1000 genomes]
rs1327988	0.81[YRI][hapmap]
rs1327989	0.82[YRI][hapmap]
rs13438513	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs13438514	0.89[YRI][hapmap]
rs17154529	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs17315334	0.81[AFR][1000 genomes]
rs17315775	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs17315929	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs17375272	0.86[AFR][1000 genomes]
rs1967332	0.87[AFR][1000 genomes]
rs2030133	0.83[AFR][1000 genomes]
rs2030134	0.83[AFR][1000 genomes]
rs2030136	0.86[YRI][hapmap];0.90[AFR][1000 genomes]
rs2031811	0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs28404962	0.81[AFR][1000 genomes]
rs28550029	0.87[AFR][1000 genomes]
rs28816386	0.82[AFR][1000 genomes]
rs28883078	0.89[AFR][1000 genomes]
rs3213853	0.90[AFR][1000 genomes]
rs3801803	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs3801805	0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs3801807	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs3801808	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs3801809	0.90[AFR][1000 genomes]
rs3801810	0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs3801812	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs3801813	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs3801814	0.90[AFR][1000 genomes]
rs3801815	0.85[AFR][1000 genomes]
rs3801816	0.90[AFR][1000 genomes]
rs3801820	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801821	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801822	0.83[AFR][1000 genomes]
rs3801825	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801826	0.83[AFR][1000 genomes]
rs3801827	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801828	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801829	0.83[AFR][1000 genomes]
rs3801830	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs3801831	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801832	0.83[AFR][1000 genomes]
rs3801833	0.83[AFR][1000 genomes]
rs3801834	0.83[AFR][1000 genomes]
rs3801837	0.83[AFR][1000 genomes]
rs3801840	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs3801842	0.82[YRI][hapmap]
rs3801843	0.81[YRI][hapmap]
rs3801844	0.81[YRI][hapmap]
rs3801848	0.82[YRI][hapmap]
rs3801850	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs3823928	0.90[AFR][1000 genomes]
rs3823930	0.83[AFR][1000 genomes]
rs3823931	0.83[AFR][1000 genomes]
rs3823932	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs3823933	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs3823936	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs3823938	0.83[AFR][1000 genomes]
rs3934268	0.90[AFR][1000 genomes]
rs4719882	0.81[AFR][1000 genomes]
rs4722644	0.81[AFR][1000 genomes]
rs4722647	0.90[AFR][1000 genomes]
rs55739485	0.83[AFR][1000 genomes]
rs56154570	0.89[AFR][1000 genomes]
rs57135974	0.83[AFR][1000 genomes]
rs58760954	0.83[AFR][1000 genomes]
rs59254259	0.83[AFR][1000 genomes]
rs61354389	0.89[AFR][1000 genomes]
rs6461980	0.90[AFR][1000 genomes]
rs6944926	0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6948657	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs73067435	0.83[AFR][1000 genomes]
rs73067443	0.83[AFR][1000 genomes]
rs73067456	0.81[AFR][1000 genomes]
rs73067475	0.83[AFR][1000 genomes]
rs73067476	0.83[AFR][1000 genomes]
rs73067479	0.80[AFR][1000 genomes]
rs73069507	0.89[AFR][1000 genomes]
rs73069510	0.89[AFR][1000 genomes]
rs7785689	0.80[AFR][1000 genomes]
rs7785798	0.83[AFR][1000 genomes]
rs7785815	0.82[AFR][1000 genomes]
rs7785832	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs7785918	0.81[AFR][1000 genomes]
rs7789225	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7791513	0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs7802715	0.81[AFR][1000 genomes]
rs7804356	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs7804620	0.90[AFR][1000 genomes]
rs7805766	0.89[YRI][hapmap];0.86[AFR][1000 genomes]

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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26867200-26897000	Weak transcription	Lung	lung
2	chr7:26870600-26896000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:26871000-26902200	Weak transcription	Dnd41	blood
4	chr7:26871600-26896000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:26872400-26896200	Weak transcription	Fetal Intestine Small	intestine
6	chr7:26875600-26896000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:26876000-26896000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:26876200-26896200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:26877200-26897000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:26877200-26897000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:26883200-26895800	Weak transcription	Adipose Nuclei	Adipose
12	chr7:26883800-26896000	Weak transcription	NHDF-Ad	bronchial
13	chr7:26886200-26903400	Weak transcription	Spleen	Spleen
14	chr7:26892800-26897200	Weak transcription	Pancreas	Pancrea
15	chr7:26893600-26896000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:26893600-26896200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:26893600-26896200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:26893600-26897800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:26894200-26895800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:26894400-26895800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:26894400-26897000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr7:26894400-26897400	Enhancers	A549	lung
23	chr7:26894600-26896400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:26895000-26895800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:26895000-26898400	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr7:26895200-26896200	Active TSS	NHEK	skin
27	chr7:26895200-26896600	Flanking Active TSS	HUVEC	blood vessel
28	chr7:26895200-26897200	Active TSS	HMEC	breast
29	chr7:26895200-26897600	Active TSS	NHLF	lung
30	chr7:26895200-26898200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:26895400-26896000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:26895400-26896200	Active TSS	Primary hematopoietic stem cells	blood
33	chr7:26895400-26896200	Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr7:26895600-26895800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:26895600-26895800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:26895600-26896000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:26895600-26897000	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links