Variant report

Variant	rs12090723
Chromosome Location	chr1:93754826-93754827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93754527..93756518-chr1:93768271..93771045,2	K562	blood:

Extended variants
information (count: 142 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1000606	0.97[EUR][1000 genomes]
rs10430073	0.97[EUR][1000 genomes]
rs10782958	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1081523	0.87[EUR][1000 genomes]
rs1081524	0.89[EUR][1000 genomes]
rs1081525	0.90[EUR][1000 genomes]
rs1081526	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10874765	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10874771	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10874774	0.92[EUR][1000 genomes]
rs10874775	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1088319	0.89[EUR][1000 genomes]
rs11164878	0.82[EUR][1000 genomes]
rs11164882	0.86[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs11164888	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164889	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164890	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164891	0.95[EUR][1000 genomes]
rs11164906	0.97[EUR][1000 genomes]
rs11164911	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11582703	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11584466	0.97[EUR][1000 genomes]
rs12057476	0.95[YRI][hapmap]
rs12070900	0.85[CEU][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12071627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12080715	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088338	0.84[EUR][1000 genomes]
rs12731675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12731809	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1323626	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1323627	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1323628	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1414367	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs1535698	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1570528	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2031223	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2031224	0.97[EUR][1000 genomes]
rs2104280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2484485	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs2749735	0.82[EUR][1000 genomes]
rs2783492	0.82[EUR][1000 genomes]
rs2783498	0.92[CEU][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs2783506	0.82[EUR][1000 genomes]
rs2815408	0.81[EUR][1000 genomes]
rs2815409	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs2815410	0.93[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs2815411	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs2815412	0.81[EUR][1000 genomes]
rs2815413	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2815414	0.85[EUR][1000 genomes]
rs4573531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4847407	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4847409	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4847411	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs485622	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs504810	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505531	0.86[EUR][1000 genomes]
rs506556	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs508942	0.96[EUR][1000 genomes]
rs512361	0.97[EUR][1000 genomes]
rs519723	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs522999	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs523262	0.95[EUR][1000 genomes]
rs546	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs556888	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs558667	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs559397	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56303209	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs566743	0.93[EUR][1000 genomes]
rs571212	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs573056	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs581825	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs587754	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs605759	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs615416	0.83[EUR][1000 genomes]
rs626714	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs628714	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs629153	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs631966	0.97[EUR][1000 genomes]
rs633789	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs637198	0.96[EUR][1000 genomes]
rs641390	0.96[EUR][1000 genomes]
rs6541351	0.93[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6541400	0.97[EUR][1000 genomes]
rs658178	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs658877	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs661566	0.91[EUR][1000 genomes]
rs662546	0.91[EUR][1000 genomes]
rs6657587	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667701	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs667680	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6687359	0.97[EUR][1000 genomes]
rs668944	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6701250	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs670650	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs671559	0.85[EUR][1000 genomes]
rs693872	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs698926	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7413775	0.97[EUR][1000 genomes]
rs7519163	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7525189	0.97[EUR][1000 genomes]
rs7529639	0.89[EUR][1000 genomes]
rs7546661	0.89[EUR][1000 genomes]
rs7551635	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7555292	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs771448	0.88[EUR][1000 genomes]
rs771449	0.89[EUR][1000 genomes]
rs771450	0.89[EUR][1000 genomes]
rs771451	0.89[EUR][1000 genomes]
rs771452	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771453	0.89[EUR][1000 genomes]
rs771456	0.92[EUR][1000 genomes]
rs771457	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771459	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs771460	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771463	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs771464	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771466	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771467	0.90[EUR][1000 genomes]
rs771468	0.90[EUR][1000 genomes]
rs771469	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs771471	0.90[EUR][1000 genomes]
rs771472	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771474	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771475	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs771477	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs771480	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs797660	0.87[EUR][1000 genomes]
rs797669	0.90[EUR][1000 genomes]
rs809515	0.89[EUR][1000 genomes]
rs810028	0.90[EUR][1000 genomes]
rs812789	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9432680	0.96[EUR][1000 genomes]
rs9432700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9432701	0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv946082	chr1:93741885-93761433	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12090723	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12090723	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12090723	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs12090723	LOC646848	cis	normal skin	skin_eQTL
rs12090723	RP4-717I23.3	cis	Whole Blood	GTEx
rs12090723	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs12090723	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs12090723	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs12090723	RP4-717I23.3	cis	Artery Aorta	GTEx
rs12090723	RP4-717I23.3	cis	Thyroid	GTEx
rs12090723	RP4-717I23.3	cis	lung	GTEx
rs12090723	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs12090723	RP4-717I23.3	cis	Artery Tibial	GTEx
rs12090723	RP4-717I23.3	cis	Stomach	GTEx
rs12090723	RP4-717I23.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:93720000-93762000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:93728600-93764400	Weak transcription	Psoas Muscle	Psoas
6	chr1:93728600-93769400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:93728600-93770400	Weak transcription	HSMM	muscle
8	chr1:93728800-93755000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:93728800-93755000	Weak transcription	Left Ventricle	heart
10	chr1:93728800-93755000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:93728800-93778200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:93729000-93790200	Weak transcription	Osteobl	bone
13	chr1:93729800-93763200	Weak transcription	Pancreas	Pancrea
14	chr1:93731000-93765400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:93731200-93787400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:93736400-93771200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:93739200-93755000	Weak transcription	HSMMtube	muscle
18	chr1:93739600-93766600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:93743600-93755400	Weak transcription	Small Intestine	intestine
20	chr1:93743600-93770200	Weak transcription	Fetal Kidney	kidney
21	chr1:93745800-93780200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:93746000-93755000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:93746600-93789400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:93746800-93780000	Weak transcription	Aorta	Aorta
25	chr1:93747800-93755000	Weak transcription	Brain Anterior Caudate	brain
26	chr1:93750800-93756800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:93751200-93761800	Weak transcription	Spleen	Spleen
28	chr1:93751400-93757200	Strong transcription	Primary T cells from cord blood	blood
29	chr1:93751600-93794600	Weak transcription	Brain Substantia Nigra	brain
30	chr1:93752000-93756600	Weak transcription	Esophagus	oesophagus
31	chr1:93752400-93755200	Weak transcription	NHLF	lung
32	chr1:93752600-93755400	Strong transcription	Primary B cells from cord blood	blood
33	chr1:93752600-93756000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr1:93752600-93756000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:93752600-93756200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:93752600-93756200	Strong transcription	Fetal Stomach	stomach
37	chr1:93752600-93757400	Weak transcription	Brain Angular Gyrus	brain
38	chr1:93752800-93755000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:93753000-93755400	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:93753000-93778200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:93753000-93803600	Weak transcription	Adipose Nuclei	Adipose
42	chr1:93753200-93806400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:93753600-93770200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:93753800-93755200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr1:93753800-93755200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:93753800-93755200	Strong transcription	Placenta	Placenta
47	chr1:93753800-93755400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:93753800-93755600	Strong transcription	Fetal Intestine Large	intestine
49	chr1:93753800-93755800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
50	chr1:93753800-93756000	ZNF genes & repeats	Primary B cells from peripheral blood	blood

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