Variant report

Variant	rs2783492
Chromosome Location	chr1:93632041-93632042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93631416..93633078-chr1:93643695..93646616,2	MCF-7	breast:
2	chr1:93619843..93621519-chr1:93631084..93633195,2	MCF-7	breast:
3	chr1:93631186..93632972-chr1:93634578..93637260,2	K562	blood:
4	chr1:93631724..93634968-chr1:93643710..93645431,3	K562	blood:

Variant related genes	Relation type
ENSG00000122483	Chromatin interaction
ENSG00000117500	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1000606	0.80[EUR][1000 genomes]
rs10430073	0.80[EUR][1000 genomes]
rs10782958	0.82[EUR][1000 genomes]
rs1081526	0.87[AMR][1000 genomes]
rs10874765	0.82[EUR][1000 genomes]
rs10874767	0.82[EUR][1000 genomes]
rs10874771	0.82[EUR][1000 genomes]
rs11164874	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11164882	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164888	0.82[EUR][1000 genomes]
rs11164889	0.82[EUR][1000 genomes]
rs11164890	0.82[EUR][1000 genomes]
rs11164906	0.80[EUR][1000 genomes]
rs11582703	0.82[EUR][1000 genomes]
rs11584466	0.80[EUR][1000 genomes]
rs11586323	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12057476	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12064785	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12066315	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12067005	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12070900	0.82[EUR][1000 genomes]
rs12071627	0.82[EUR][1000 genomes]
rs12080715	0.82[EUR][1000 genomes]
rs12085959	0.82[EUR][1000 genomes]
rs12087466	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12088338	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12090723	0.82[EUR][1000 genomes]
rs12094547	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12731675	0.82[EUR][1000 genomes]
rs12731809	0.82[EUR][1000 genomes]
rs1323626	0.87[AMR][1000 genomes]
rs1323628	0.84[AMR][1000 genomes]
rs1414367	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1535698	0.82[EUR][1000 genomes]
rs17131699	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2031224	0.80[EUR][1000 genomes]
rs2104280	0.81[EUR][1000 genomes]
rs2391227	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2484485	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2749735	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2783498	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2783506	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2815408	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815409	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815410	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815411	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815412	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2815413	0.90[EUR][1000 genomes]
rs2815414	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36057148	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4573531	0.82[EUR][1000 genomes]
rs4847407	0.81[EUR][1000 genomes]
rs4847409	0.80[EUR][1000 genomes]
rs485622	0.83[EUR][1000 genomes]
rs504810	0.81[EUR][1000 genomes]
rs505531	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs506556	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs512361	0.80[EUR][1000 genomes]
rs519723	0.82[EUR][1000 genomes]
rs522999	0.90[EUR][1000 genomes]
rs546	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs556888	0.80[EUR][1000 genomes]
rs55701931	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs558667	0.82[EUR][1000 genomes]
rs559397	0.82[EUR][1000 genomes]
rs56303209	0.82[EUR][1000 genomes]
rs571212	0.83[EUR][1000 genomes]
rs573056	0.88[EUR][1000 genomes]
rs581825	0.89[EUR][1000 genomes]
rs587754	0.82[EUR][1000 genomes]
rs605759	0.84[EUR][1000 genomes]
rs615416	0.90[EUR][1000 genomes]
rs626714	0.82[EUR][1000 genomes]
rs629153	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs631966	0.80[EUR][1000 genomes]
rs633789	0.80[EUR][1000 genomes]
rs6541400	0.80[EUR][1000 genomes]
rs658178	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs658877	0.90[EUR][1000 genomes]
rs661566	0.81[EUR][1000 genomes]
rs662546	0.81[EUR][1000 genomes]
rs6657587	0.82[EUR][1000 genomes]
rs6667701	0.82[EUR][1000 genomes]
rs667680	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6687359	0.80[EUR][1000 genomes]
rs670650	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs671559	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs693872	0.80[EUR][1000 genomes]
rs698926	0.87[AMR][1000 genomes]
rs71510760	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7413775	0.80[EUR][1000 genomes]
rs7519163	0.80[EUR][1000 genomes]
rs7525189	0.80[EUR][1000 genomes]
rs7551635	0.82[EUR][1000 genomes]
rs7555292	0.82[EUR][1000 genomes]
rs771452	0.87[AMR][1000 genomes]
rs771457	0.87[AMR][1000 genomes]
rs771460	0.87[AMR][1000 genomes]
rs771464	0.81[AMR][1000 genomes]
rs771466	0.87[AMR][1000 genomes]
rs771472	0.87[AMR][1000 genomes]
rs771474	0.87[AMR][1000 genomes]
rs771480	0.87[AMR][1000 genomes]
rs797660	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs797669	0.80[EUR][1000 genomes]
rs809515	0.83[EUR][1000 genomes]
rs9432700	0.82[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2783492	RP4-717I23.3	cis	lung	GTEx
rs2783492	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs2783492	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs2783492	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs2783492	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2783492	RP4-717I23.3	cis	Whole Blood	GTEx
rs2783492	RP4-717I23.3	cis	Thyroid	GTEx
rs2783492	RP4-717I23.3	cis	Artery Tibial	GTEx
rs2783492	RP4-717I23.3	cis	Stomach	GTEx
rs2783492	RP4-717I23.3	cis	Artery Aorta	GTEx
rs2783492	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs2783492	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs2783492	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs2783492	TMED5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:93582400-93642800	Weak transcription	Gastric	stomach
3	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
4	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
5	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
7	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
8	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:93614200-93634800	Weak transcription	A549	lung
13	chr1:93615600-93643200	Weak transcription	Fetal Kidney	kidney
14	chr1:93620800-93635600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:93621400-93632200	Weak transcription	Fetal Stomach	stomach
16	chr1:93621400-93635400	Weak transcription	Thymus	Thymus
17	chr1:93621400-93635600	Weak transcription	Lung	lung
18	chr1:93621400-93636800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:93621400-93637800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:93621400-93640000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:93621400-93643000	Weak transcription	HMEC	breast
22	chr1:93621400-93643800	Weak transcription	Colonic Mucosa	Colon
23	chr1:93621600-93641400	Weak transcription	NHEK	skin
24	chr1:93622200-93637200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:93622400-93636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:93623200-93633200	Weak transcription	Hela-S3	cervix
27	chr1:93624000-93637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:93624000-93643400	Weak transcription	NH-A	brain
29	chr1:93624000-93643600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:93624200-93636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:93624400-93643600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:93624800-93636400	Weak transcription	Primary T cells from cord blood	blood
33	chr1:93624800-93641600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:93624800-93643600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:93624800-93643600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:93625000-93636600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:93625000-93640000	Weak transcription	K562	blood
38	chr1:93625000-93641200	Weak transcription	HSMM	muscle
39	chr1:93625200-93635400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:93625200-93637200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:93625400-93636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:93625600-93634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:93625600-93634800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:93625600-93637600	Weak transcription	NHLF	lung
45	chr1:93625800-93632400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:93625800-93632400	Weak transcription	Fetal Intestine Large	intestine
47	chr1:93625800-93633200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:93625800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:93625800-93635800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:93625800-93637000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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