Variant report

Variant	rs12490933
Chromosome Location	chr3:17754925-17754926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:17753992..17758136-chr3:17779432..17782585,3	K562	blood:
2	chr3:17753447..17755867-chr3:17768975..17771432,2	K562	blood:
3	chr3:17747018..17749976-chr3:17753011..17756693,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131374	Chromatin interaction
ENSG00000233133	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs10433560	0.81[EUR][1000 genomes]
rs10433561	0.85[EUR][1000 genomes]
rs10510477	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10510478	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11128836	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11128837	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11128838	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11128840	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11128841	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11128842	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11128843	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11128844	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11128848	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11128849	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11128850	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11128852	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11708672	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719266	0.84[EUR][1000 genomes]
rs11719326	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11927637	0.83[EUR][1000 genomes]
rs11927654	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11929111	0.86[EUR][1000 genomes]
rs12487248	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12487916	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12488591	0.83[EUR][1000 genomes]
rs12497320	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12631291	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12632570	0.86[EUR][1000 genomes]
rs12634674	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12634893	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13061771	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13065637	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13069155	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13071728	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13071934	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13076724	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13079096	0.91[EUR][1000 genomes]
rs13083917	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13085167	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13096559	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13097908	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13320647	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34002492	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34297417	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34485427	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34487714	0.86[EUR][1000 genomes]
rs34786175	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34990533	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35460334	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35642812	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35697509	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36172181	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4128509	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4243835	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4243836	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4243837	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4243838	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4312680	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4349529	0.91[EUR][1000 genomes]
rs4377510	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4408889	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4431138	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4435673	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4435674	0.82[EUR][1000 genomes]
rs4444738	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4470554	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4482690	0.86[EUR][1000 genomes]
rs4484221	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4488868	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4513482	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4566567	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4566568	0.82[EUR][1000 genomes]
rs4568172	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4589965	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4602424	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4611850	0.91[EUR][1000 genomes]
rs4637311	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4643736	0.90[EUR][1000 genomes]
rs4908938	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4908940	0.82[EUR][1000 genomes]
rs4908958	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4908963	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4908964	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4908965	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4908966	0.86[EUR][1000 genomes]
rs4908967	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4908968	0.95[EUR][1000 genomes]
rs4908969	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4908970	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4908971	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4908972	0.81[EUR][1000 genomes]
rs4908973	0.82[EUR][1000 genomes]
rs4908987	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4908992	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4909009	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4909010	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4909012	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5014632	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55701200	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56059241	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57309958	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61081795	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61236237	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6577616	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6577617	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6577618	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6577619	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6577622	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6577643	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6577644	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6768637	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6779834	0.83[EUR][1000 genomes]
rs6780587	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6784025	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6789467	0.91[EUR][1000 genomes]
rs6789697	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6792422	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6795189	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6796448	0.82[EUR][1000 genomes]
rs6797952	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6803312	0.87[EUR][1000 genomes]
rs6804837	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6806610	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6807020	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6809062	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6810235	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7431897	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7613953	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7617683	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7622878	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7627064	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7627732	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7630695	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7632240	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7633601	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7645459	0.83[EUR][1000 genomes]
rs7647914	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7647928	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7650617	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7651998	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7652156	0.84[EUR][1000 genomes]
rs8179891	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8179983	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9310524	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9310526	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9310528	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9681232	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9681617	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9681644	0.82[AMR][1000 genomes]
rs9681893	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9756494	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9757339	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9815204	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9816920	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9821318	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9821955	0.80[EUR][1000 genomes]
rs9823767	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9839588	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9847477	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9853571	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9857910	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9860854	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9867064	0.82[EUR][1000 genomes]
rs9875973	0.86[EUR][1000 genomes]
rs9880456	0.86[EUR][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	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1828838	chr3:17646794-17757960	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv999594	chr3:17690416-17982318	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17711400-17755000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:17731600-17755600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:17732600-17755400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:17733200-17755600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:17735200-17755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:17735200-17755800	Weak transcription	Lung	lung
7	chr3:17735400-17755400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:17735400-17755600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:17735400-17755800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:17744400-17755600	Weak transcription	Left Ventricle	heart
11	chr3:17745200-17755800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:17745400-17755400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:17746200-17755600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:17746800-17755800	Weak transcription	Esophagus	oesophagus
15	chr3:17747000-17756800	Weak transcription	Colonic Mucosa	Colon
16	chr3:17747400-17755400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:17747800-17755200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:17748000-17755200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:17748000-17755400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:17748000-17755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:17748000-17755800	Weak transcription	Fetal Intestine Small	intestine
22	chr3:17748000-17756000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:17748200-17755200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:17748200-17755200	Weak transcription	Dnd41	blood
25	chr3:17748400-17755400	Weak transcription	Primary T cells from cord blood	blood
26	chr3:17749400-17755600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:17749600-17755200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:17749600-17755200	Weak transcription	A549	lung
29	chr3:17749800-17755400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:17749800-17755400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:17749800-17756200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:17751400-17756000	Weak transcription	Small Intestine	intestine
33	chr3:17751600-17755400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:17752000-17755800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:17752000-17762000	Weak transcription	Right Ventricle	heart
36	chr3:17753600-17755400	Weak transcription	Fetal Thymus	thymus
37	chr3:17753800-17755800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:17753800-17758200	ZNF genes & repeats	GM12878-XiMat	blood
39	chr3:17754000-17755200	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:17754000-17755600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:17754000-17755600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:17754000-17755800	Weak transcription	Ovary	ovary
43	chr3:17754200-17755400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:17754400-17755600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:17754600-17755200	Weak transcription	Primary B cells from cord blood	blood

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