Variant report

Variant	rs10280476
Chromosome Location	chr7:26899002-26899003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26897524..26906359-chr7:27169396..27177834,18	MCF-7	breast:
2	chr7:26897800..26900077-chr7:26902564..26904395,2	MCF-7	breast:
3	chr7:26898807..26900434-chr7:27171032..27173228,2	MCF-7	breast:
4	chr7:26898402..26900305-chr7:26902802..26904854,2	MCF-7	breast:
5	chr7:26894872..26897680-chr7:26898769..26901003,2	K562	blood:
6	chr7:26897760..26899796-chr7:26902533..26905235,3	K562	blood:

Variant related genes	Relation type
ENSG00000197576	Chromatin interaction
ENSG00000254369	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]
rs10259983	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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]
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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26871000-26902200	Weak transcription	Dnd41	blood
2	chr7:26886200-26903400	Weak transcription	Spleen	Spleen
3	chr7:26896400-26902600	Weak transcription	NHDF-Ad	bronchial
4	chr7:26897800-26899400	Enhancers	HepG2	liver
5	chr7:26898000-26899200	Enhancers	HUVEC	blood vessel
6	chr7:26898000-26900200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:26898000-26902600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:26898200-26901000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr7:26898400-26899200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr7:26898400-26899400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:26898400-26900200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:26898400-26901800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:26898600-26900200	Weak transcription	Primary B cells from cord blood	blood
14	chr7:26898600-26900400	Enhancers	HMEC	breast
15	chr7:26898600-26900800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr7:26898600-26902200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:26898600-26902200	Enhancers	NHEK	skin
18	chr7:26898600-26902600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:26898800-26899800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:26898800-26900000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr7:26898800-26900000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:26898800-26900000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:26898800-26900000	Weak transcription	A549	lung
24	chr7:26898800-26900000	Weak transcription	GM12878-XiMat	blood
25	chr7:26898800-26900600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:26898800-26900600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:26898800-26902200	Weak transcription	Adipose Nuclei	Adipose
28	chr7:26898800-26903200	Weak transcription	Colonic Mucosa	Colon
29	chr7:26898800-26903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:26898800-26903400	Weak transcription	Psoas Muscle	Psoas
31	chr7:26898800-26903600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:26899000-26899200	Enhancers	Fetal Intestine Small	intestine
33	chr7:26899000-26900000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:26899000-26900000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:26899000-26902600	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links