Variant report

Variant	rs10875895
Chromosome Location	chr12:49316742-49316743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49314886..49317181-chr12:49317184..49320260,3	MCF-7	breast:
2	chr12:49316284..49318083-chr12:49329408..49331659,2	MCF-7	breast:
3	chr12:49312309..49314599-chr12:49315946..49318306,2	MCF-7	breast:
4	chr12:49246426..49247989-chr12:49314657..49316917,2	MCF-7	breast:
5	chr12:49258143..49260662-chr12:49316104..49319150,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134285	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1051886	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1054376	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747556	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747557	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747558	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783289	0.95[ASN][1000 genomes]
rs10783290	0.93[ASN][1000 genomes]
rs10783292	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783293	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10783294	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783295	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783297	0.92[ASN][1000 genomes]
rs10875886	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875888	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875892	0.81[ASN][1000 genomes]
rs10875893	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875894	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875896	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875897	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875898	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875900	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875901	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875902	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1111662	0.92[ASN][1000 genomes]
rs11168779	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168783	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168784	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168785	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168790	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168795	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168797	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168798	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168800	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168801	0.85[ASN][1000 genomes]
rs11168803	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168811	0.80[ASN][1000 genomes]
rs11168812	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608916	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610459	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610497	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614474	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227240	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12228521	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229275	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423542	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579249	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1318692	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1690182	0.90[ASN][1000 genomes]
rs1818996	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1830192	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030900	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070940	0.90[ASN][1000 genomes]
rs2073480	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131713	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272311	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293449	0.97[ASN][1000 genomes]
rs2368701	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453063	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2463175	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2641450	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2694839	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2694840	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741627	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782353	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809147	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825182	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825184	0.99[ASN][1000 genomes]
rs4018510	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4433614	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4526804	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760647	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760661	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760662	0.84[EUR][1000 genomes]
rs4760663	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760664	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760665	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760666	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760667	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760668	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58023472	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59087236	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61941142	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61942166	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942167	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61942169	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61942207	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942209	0.81[ASN][1000 genomes]
rs6580696	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134686	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297958	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7298330	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304942	1.00[ASN][1000 genomes]
rs7313988	0.90[ASN][1000 genomes]
rs7489036	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963018	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7963160	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7976473	0.86[ASN][1000 genomes]
rs833820	0.90[ASN][1000 genomes]
rs833821	0.90[ASN][1000 genomes]
rs833822	0.90[ASN][1000 genomes]
rs833827	0.90[ASN][1000 genomes]
rs833828	0.88[ASN][1000 genomes]
rs833839	0.84[ASN][1000 genomes]
rs833840	0.84[ASN][1000 genomes]
rs833841	0.83[ASN][1000 genomes]
rs833842	0.83[ASN][1000 genomes]
rs833843	0.80[ASN][1000 genomes]
rs961320	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9645813	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9783452	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783477	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788029	0.96[ASN][1000 genomes]
rs9795742	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9796008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875895	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49298200-49318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:49298400-49317800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:49298400-49318000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:49298400-49318000	Weak transcription	Brain Substantia Nigra	brain
5	chr12:49298400-49318000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:49298400-49318200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:49298400-49318200	Weak transcription	Right Atrium	heart
8	chr12:49298400-49318400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:49298600-49318200	Weak transcription	Brain Anterior Caudate	brain
10	chr12:49298800-49318000	Weak transcription	Fetal Lung	lung
11	chr12:49298800-49318200	Weak transcription	Fetal Brain Male	brain
12	chr12:49302000-49318200	Weak transcription	Brain Germinal Matrix	brain
13	chr12:49302800-49317800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:49305000-49318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:49305200-49317600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:49307800-49318200	Weak transcription	Brain Angular Gyrus	brain
17	chr12:49308800-49318200	Weak transcription	Fetal Brain Female	brain
18	chr12:49309000-49317800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:49310000-49318200	Weak transcription	Gastric	stomach
20	chr12:49310600-49318000	Weak transcription	Fetal Intestine Large	intestine
21	chr12:49311000-49318600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:49311800-49317800	Weak transcription	Spleen	Spleen
23	chr12:49311800-49317800	Weak transcription	HSMM	muscle
24	chr12:49312000-49318000	Weak transcription	HepG2	liver
25	chr12:49312000-49318200	Weak transcription	Fetal Kidney	kidney
26	chr12:49312200-49318200	Weak transcription	Primary B cells from cord blood	blood
27	chr12:49312400-49318200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:49312600-49317000	Weak transcription	HSMMtube	muscle
29	chr12:49312600-49317800	Weak transcription	HUVEC	blood vessel
30	chr12:49312600-49318000	Weak transcription	Thymus	Thymus
31	chr12:49313000-49317600	Weak transcription	Fetal Thymus	thymus
32	chr12:49313000-49317800	Weak transcription	Dnd41	blood
33	chr12:49313000-49318000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:49313200-49318200	Weak transcription	Colonic Mucosa	Colon
35	chr12:49313200-49318200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:49313400-49317800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:49313400-49318000	Weak transcription	HMEC	breast
38	chr12:49313400-49318400	Weak transcription	Left Ventricle	heart
39	chr12:49313400-49318400	Weak transcription	Ovary	ovary
40	chr12:49313400-49319000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:49313600-49318200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:49313600-49318200	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:49313600-49318200	Weak transcription	NHDF-Ad	bronchial
44	chr12:49313600-49318400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:49313800-49317800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr12:49314200-49318000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:49314400-49317200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr12:49314400-49317200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:49314400-49318000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:49314400-49318200	Weak transcription	Placenta	Placenta

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