Variant report

Variant	rs10875964
Chromosome Location	chr12:50080910-50080911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50080427..50082261-chr12:50100297..50101923,2	MCF-7	breast:
2	chr12:50080406..50083815-chr12:50089731..50092749,3	MCF-7	breast:
3	chr12:50080143..50085132-chr12:50089232..50093203,6	K562	blood:
4	chr12:50080608..50083488-chr12:50095334..50097821,2	MCF-7	breast:
5	chr12:50080058..50082112-chr12:50085223..50087570,2	MCF-7	breast:
6	chr12:50037476..50040011-chr12:50080826..50083023,2	MCF-7	breast:
7	chr12:50073227..50075348-chr12:50080508..50083212,2	MCF-7	breast:
8	chr12:50080839..50082348-chr12:50098769..50100766,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction
ENSG00000161791	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1049986	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875968	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11169065	0.81[EUR][1000 genomes]
rs11169069	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169070	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11169073	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169076	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169081	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169082	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169092	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169097	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169101	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169104	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169106	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169109	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169111	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169112	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169113	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11169118	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169125	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169127	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11169133	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169140	0.85[AMR][1000 genomes]
rs11615488	0.92[ASN][1000 genomes]
rs11833411	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11834380	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12296586	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299505	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12299513	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12301824	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12303310	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304796	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12305460	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12308256	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12309940	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310510	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311839	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12314795	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314878	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12315224	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315791	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316284	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12317646	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320556	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12321169	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12321819	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13066	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13906	0.83[ASN][1000 genomes]
rs1470906	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574326	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123808	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1902329	0.82[EUR][1000 genomes]
rs1902330	0.80[EUR][1000 genomes]
rs2005195	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2241418	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278068	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278069	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278070	0.80[ASN][1000 genomes]
rs2303305	0.80[ASN][1000 genomes]
rs2336058	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878532	0.89[AMR][1000 genomes]
rs3815832	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3887728	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4045193	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4073998	0.82[AMR][1000 genomes]
rs4133070	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584654	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs52824916	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs55853522	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57191490	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57342147	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57463238	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57916875	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58278271	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58446833	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59233136	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59849800	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59940006	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60121503	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60402517	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61512987	0.85[AMR][1000 genomes]
rs61616163	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61620972	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61710637	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580719	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131915	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7136052	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137976	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296281	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7299002	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301209	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7306877	0.83[ASN][1000 genomes]
rs7309607	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7312658	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7313738	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305008	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73305012	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73305085	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73305098	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73306808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73309030	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74089182	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7688	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952734	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953911	0.83[ASN][1000 genomes]
rs7954994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955586	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7956089	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956181	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962645	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962863	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7963954	0.89[ASN][1000 genomes]
rs7965658	0.81[ASN][1000 genomes]
rs7967624	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7970241	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7973389	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7975599	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7977389	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7979262	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980979	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876889	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs897056	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9804749	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804971	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50068600-50083600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:50070000-50083400	Weak transcription	Brain Substantia Nigra	brain
3	chr12:50074400-50081800	Weak transcription	Right Ventricle	heart
4	chr12:50075800-50082600	Weak transcription	Primary B cells from cord blood	blood
5	chr12:50077000-50082800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:50077000-50084600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:50077400-50086200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:50078000-50087600	Weak transcription	Placenta	Placenta
9	chr12:50078000-50091000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:50078200-50081600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:50078200-50083400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:50078200-50083600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:50078400-50081600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:50078400-50083200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:50078600-50082000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:50078600-50082000	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:50078600-50083400	Weak transcription	Fetal Thymus	thymus
18	chr12:50078600-50090600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:50078600-50092200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:50078800-50081400	Weak transcription	Primary T cells from cord blood	blood
21	chr12:50078800-50081400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:50078800-50081400	Weak transcription	Osteobl	bone
23	chr12:50078800-50081600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:50078800-50081800	Weak transcription	Fetal Lung	lung
25	chr12:50078800-50081800	Weak transcription	Right Atrium	heart
26	chr12:50078800-50083000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:50078800-50083000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:50078800-50083400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:50078800-50083600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:50078800-50083600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:50078800-50083600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:50078800-50083600	Weak transcription	Spleen	Spleen
33	chr12:50078800-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:50078800-50088200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:50078800-50088200	Weak transcription	HSMM	muscle
36	chr12:50078800-50091800	Weak transcription	NH-A	brain
37	chr12:50078800-50092400	Weak transcription	NHLF	lung
38	chr12:50079000-50081600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:50079000-50081600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:50079000-50081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:50079000-50081600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:50079000-50083200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:50079000-50083200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:50079000-50088000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:50079000-50088000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:50079000-50092000	Weak transcription	Small Intestine	intestine
47	chr12:50079000-50096200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:50079200-50081600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:50079200-50081600	Weak transcription	Left Ventricle	heart
50	chr12:50079200-50081800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links