Variant report

Variant	rs12695654
Chromosome Location	chr3:136568531-136568532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136567416..136569701-chr3:136569740..136571267,2	MCF-7	breast:
2	chr3:136568394..136571514-chr3:136574804..136577535,3	K562	blood:
3	chr3:136559234..136561266-chr3:136568039..136570871,2	K562	blood:
4	chr3:136568386..136570970-chr3:136579432..136581354,2	K562	blood:

Variant related genes	Relation type
ENSG00000239213	Chromatin interaction
ENSG00000158092	Chromatin interaction

Extended variants
information (count: 160 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs10470440	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1052618	0.87[EUR][1000 genomes]
rs10935198	0.88[EUR][1000 genomes]
rs10935210	0.82[EUR][1000 genomes]
rs11924477	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12330283	0.84[EUR][1000 genomes]
rs12487901	0.82[EUR][1000 genomes]
rs12488365	0.84[EUR][1000 genomes]
rs12491278	0.81[EUR][1000 genomes]
rs12491729	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12491730	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12497379	0.88[EUR][1000 genomes]
rs12630955	0.85[EUR][1000 genomes]
rs12633003	0.84[EUR][1000 genomes]
rs12633073	0.80[EUR][1000 genomes]
rs12637949	0.84[EUR][1000 genomes]
rs12695653	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13315318	0.83[EUR][1000 genomes]
rs1344790	0.82[EUR][1000 genomes]
rs1400261	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1406540	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1406541	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1569228	0.88[EUR][1000 genomes]
rs1569229	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1805300	0.88[EUR][1000 genomes]
rs1865149	0.83[EUR][1000 genomes]
rs1914048	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1965108	0.83[EUR][1000 genomes]
rs1965109	0.82[EUR][1000 genomes]
rs1971788	0.83[EUR][1000 genomes]
rs2031029	0.84[EUR][1000 genomes]
rs2031030	0.87[EUR][1000 genomes]
rs2060303	0.87[EUR][1000 genomes]
rs2117010	0.84[EUR][1000 genomes]
rs2138540	0.84[EUR][1000 genomes]
rs2138541	0.84[EUR][1000 genomes]
rs2271684	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2343662	0.83[EUR][1000 genomes]
rs2343663	0.83[EUR][1000 genomes]
rs28564581	0.85[EUR][1000 genomes]
rs28672119	0.86[EUR][1000 genomes]
rs28761333	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2880767	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35339486	0.84[EUR][1000 genomes]
rs35760633	0.84[EUR][1000 genomes]
rs3772387	0.83[EUR][1000 genomes]
rs3772388	0.83[EUR][1000 genomes]
rs3845925	0.81[EUR][1000 genomes]
rs3856623	0.83[EUR][1000 genomes]
rs3915455	0.83[EUR][1000 genomes]
rs3963921	0.83[EUR][1000 genomes]
rs4038076	0.87[EUR][1000 genomes]
rs4038077	0.83[EUR][1000 genomes]
rs4533585	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4678272	0.84[EUR][1000 genomes]
rs4678273	0.84[EUR][1000 genomes]
rs4678274	0.84[EUR][1000 genomes]
rs4678276	0.81[EUR][1000 genomes]
rs4678443	0.87[EUR][1000 genomes]
rs4678444	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4678445	0.87[EUR][1000 genomes]
rs4678448	0.88[EUR][1000 genomes]
rs4678450	0.84[EUR][1000 genomes]
rs4678451	0.84[EUR][1000 genomes]
rs4678452	0.84[EUR][1000 genomes]
rs6439663	0.87[EUR][1000 genomes]
rs6439664	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6439667	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6439670	0.87[EUR][1000 genomes]
rs6439671	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6439672	0.87[EUR][1000 genomes]
rs6439673	0.84[EUR][1000 genomes]
rs6766755	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6771717	0.83[EUR][1000 genomes]
rs6773117	0.88[EUR][1000 genomes]
rs6775389	0.81[EUR][1000 genomes]
rs6777816	0.87[EUR][1000 genomes]
rs6783508	0.84[EUR][1000 genomes]
rs6783999	0.83[EUR][1000 genomes]
rs6784005	0.84[EUR][1000 genomes]
rs6786302	0.83[EUR][1000 genomes]
rs6786648	0.84[EUR][1000 genomes]
rs6793966	0.81[EUR][1000 genomes]
rs6797509	0.87[EUR][1000 genomes]
rs6800032	0.84[EUR][1000 genomes]
rs6809943	0.87[EUR][1000 genomes]
rs7431100	0.83[EUR][1000 genomes]
rs7611847	0.82[EUR][1000 genomes]
rs7614422	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7617932	0.84[EUR][1000 genomes]
rs7627443	0.87[EUR][1000 genomes]
rs7629882	0.84[EUR][1000 genomes]
rs7630571	0.86[EUR][1000 genomes]
rs7631017	0.84[EUR][1000 genomes]
rs7645773	0.84[EUR][1000 genomes]
rs7647451	0.83[EUR][1000 genomes]
rs7648817	0.83[EUR][1000 genomes]
rs7649211	0.86[EUR][1000 genomes]
rs7651644	0.82[EUR][1000 genomes]
rs856662	0.81[EUR][1000 genomes]
rs9289518	0.88[EUR][1000 genomes]
rs9289519	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9289520	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs938525	0.87[EUR][1000 genomes]
rs9682106	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9811169	0.83[EUR][1000 genomes]
rs9815771	0.84[EUR][1000 genomes]
rs9817118	0.84[EUR][1000 genomes]
rs9817132	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9817453	0.88[EUR][1000 genomes]
rs9818397	0.88[EUR][1000 genomes]
rs9818792	0.84[EUR][1000 genomes]
rs9819572	0.88[EUR][1000 genomes]
rs9819743	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9819804	0.88[EUR][1000 genomes]
rs9821557	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9823565	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9827648	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9832045	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9833952	0.81[EUR][1000 genomes]
rs9834250	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9834438	0.82[EUR][1000 genomes]
rs9834861	0.84[EUR][1000 genomes]
rs9835096	0.86[EUR][1000 genomes]
rs9836807	0.87[EUR][1000 genomes]
rs9838022	0.84[EUR][1000 genomes]
rs9841985	0.83[EUR][1000 genomes]
rs9842436	0.84[EUR][1000 genomes]
rs9842577	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9843352	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9843733	0.84[EUR][1000 genomes]
rs9846334	0.84[EUR][1000 genomes]
rs9846691	0.84[EUR][1000 genomes]
rs9846754	0.82[EUR][1000 genomes]
rs9847548	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9848867	0.84[EUR][1000 genomes]
rs9849767	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9851726	0.83[EUR][1000 genomes]
rs9853417	0.84[EUR][1000 genomes]
rs9855314	0.82[EUR][1000 genomes]
rs9856828	0.84[EUR][1000 genomes]
rs9859665	0.84[EUR][1000 genomes]
rs9860774	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9863551	0.82[EUR][1000 genomes]
rs9864926	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9864941	0.84[EUR][1000 genomes]
rs9865545	0.88[EUR][1000 genomes]
rs9871987	0.85[EUR][1000 genomes]
rs9874887	0.84[EUR][1000 genomes]
rs9878117	0.84[EUR][1000 genomes]
rs9878367	0.84[EUR][1000 genomes]
rs9878464	0.84[EUR][1000 genomes]
rs9880708	0.83[EUR][1000 genomes]
rs9883108	0.82[EUR][1000 genomes]
rs9883131	0.83[EUR][1000 genomes]
rs9883979	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12695654	RP11-85F14.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136551600-136574000	Weak transcription	HepG2	liver
2	chr3:136552400-136570800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:136552600-136579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:136554800-136578400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:136554800-136579400	Weak transcription	Fetal Lung	lung
6	chr3:136555000-136574000	Weak transcription	Ovary	ovary
7	chr3:136555400-136579200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:136555600-136577800	Weak transcription	Lung	lung
9	chr3:136555600-136579200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:136555600-136580000	Weak transcription	Esophagus	oesophagus
11	chr3:136556000-136573400	Weak transcription	GM12878-XiMat	blood
12	chr3:136558200-136575600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:136558200-136579200	Weak transcription	NHDF-Ad	bronchial
14	chr3:136558400-136573600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:136558400-136579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:136558400-136579400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:136558400-136579600	Weak transcription	NHEK	skin
18	chr3:136558600-136570800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:136558600-136573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:136558600-136575600	Weak transcription	Aorta	Aorta
21	chr3:136558600-136578000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:136558600-136578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:136558600-136578800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:136558600-136579200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:136558600-136579200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:136558600-136579600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:136558600-136579600	Weak transcription	Liver	Liver
28	chr3:136558600-136579600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:136558600-136579600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:136558600-136579800	Weak transcription	HSMM	muscle
31	chr3:136558800-136573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:136558800-136573800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:136558800-136574000	Weak transcription	Brain Germinal Matrix	brain
34	chr3:136558800-136578600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:136558800-136578800	Weak transcription	HMEC	breast
36	chr3:136558800-136579000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:136558800-136579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:136558800-136579400	Weak transcription	Pancreas	Pancrea
39	chr3:136559000-136573600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:136559000-136575400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:136559000-136579400	Weak transcription	Brain Angular Gyrus	brain
42	chr3:136559000-136579600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:136559000-136580000	Weak transcription	Left Ventricle	heart
44	chr3:136559200-136573400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:136559200-136573800	Weak transcription	Fetal Brain Female	brain
46	chr3:136559200-136575800	Weak transcription	Right Atrium	heart
47	chr3:136559200-136579400	Weak transcription	Right Ventricle	heart
48	chr3:136559200-136579800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:136559400-136573400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:136559400-136573400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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