Variant report

Variant	rs12229275
Chromosome Location	chr12:49325840-49325841
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49324577..49326698-chr12:49333742..49335694,2	K562	blood:
2	chr12:49107528..49110238-chr12:49323748..49326507,2	MCF-7	breast:
3	chr12:49317829..49322118-chr12:49322940..49327806,7	MCF-7	breast:
4	chr12:49316245..49319043-chr12:49323994..49326316,2	K562	blood:

Variant related genes	Relation type
ENSG00000129315	Chromatin interaction
ENSG00000134285	Chromatin interaction
ENSG00000201678	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	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1054376	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747556	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747557	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747558	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10783289	0.92[ASN][1000 genomes]
rs10783290	0.90[ASN][1000 genomes]
rs10783292	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783293	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783294	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783295	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783297	0.92[ASN][1000 genomes]
rs10875886	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10875888	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875892	0.81[AMR][1000 genomes]
rs10875893	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875894	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875895	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875896	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875897	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875898	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875900	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875901	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875902	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1111662	0.92[ASN][1000 genomes]
rs11168779	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168783	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168784	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168785	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168790	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168792	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168794	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168795	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168797	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168798	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168800	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168801	0.85[ASN][1000 genomes]
rs11168803	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168811	0.80[ASN][1000 genomes]
rs11168812	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608916	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610459	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11610497	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11614474	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227240	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12228521	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12423542	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579249	0.96[ASN][1000 genomes]
rs1318692	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1690182	0.90[ASN][1000 genomes]
rs1818996	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1830192	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030900	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070940	0.90[ASN][1000 genomes]
rs2073480	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131713	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272311	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272312	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293449	0.95[ASN][1000 genomes]
rs2368701	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453063	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2463175	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2641450	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2694839	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2694840	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741627	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759146	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782353	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809147	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825182	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825184	0.94[ASN][1000 genomes]
rs4018510	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237854	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4433614	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4526804	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760600	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760647	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4760661	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760662	0.83[EUR][1000 genomes]
rs4760663	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760664	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760665	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760666	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760667	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760668	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58023472	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59087236	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61941142	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61942166	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942167	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61942169	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61942207	0.83[AMR][1000 genomes];0.88[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	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297958	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7298330	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7304942	0.96[ASN][1000 genomes]
rs7313988	0.90[ASN][1000 genomes]
rs7489036	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7963018	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7963160	0.80[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	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9645813	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9783452	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783477	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788029	0.96[ASN][1000 genomes]
rs9795742	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9796008	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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
rs12229275	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49314400-49338000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:49314400-49338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:49319200-49349800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:49319400-49337800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:49319600-49326600	Weak transcription	Aorta	Aorta
6	chr12:49319600-49331800	Weak transcription	Psoas Muscle	Psoas
7	chr12:49319600-49332800	Weak transcription	Small Intestine	intestine
8	chr12:49319600-49334600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:49319800-49326000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:49319800-49326200	Weak transcription	Colonic Mucosa	Colon
11	chr12:49319800-49326200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:49319800-49326400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:49319800-49326400	Weak transcription	Ovary	ovary
14	chr12:49319800-49326400	Weak transcription	Pancreas	Pancrea
15	chr12:49319800-49326600	Weak transcription	Fetal Brain Male	brain
16	chr12:49319800-49326600	Weak transcription	Gastric	stomach
17	chr12:49319800-49326800	Weak transcription	Right Ventricle	heart
18	chr12:49319800-49328000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:49319800-49328800	Weak transcription	Fetal Heart	heart
20	chr12:49319800-49331400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:49319800-49333200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:49319800-49349400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:49320000-49326400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:49320000-49326400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:49320800-49329800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:49320800-49333400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:49320800-49333600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:49320800-49335800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:49320800-49336000	Strong transcription	A549	lung
30	chr12:49320800-49338600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:49321000-49330200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:49321000-49332200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:49321000-49333400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:49321000-49334200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:49321000-49335000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:49321000-49335600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:49321000-49335800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:49321000-49336400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:49321000-49336800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:49321000-49338200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:49321200-49326200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:49321200-49332200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr12:49321400-49328800	Weak transcription	Stomach Mucosa	stomach
44	chr12:49321400-49334200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:49321600-49334600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:49321800-49337800	Strong transcription	Fetal Intestine Small	intestine
47	chr12:49322800-49328200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr12:49322800-49329200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:49322800-49335200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr12:49322800-49337600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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