Variant report

Variant	rs559397
Chromosome Location	chr1:93729008-93729009
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93728185..93731169-chr1:93735951..93738017,2	MCF-7	breast:
2	chr1:93725585..93728395-chr1:93728407..93730397,2	MCF-7	breast:

Extended variants
information (count: 141 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1000606	0.97[EUR][1000 genomes]
rs10430073	0.97[EUR][1000 genomes]
rs10782958	0.91[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10874767	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10874771	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10874774	0.92[EUR][1000 genomes]
rs10874775	0.82[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	0.82[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	0.92[EUR][1000 genomes]
rs11582703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11584466	0.97[EUR][1000 genomes]
rs12070900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12071627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12080715	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12085959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088338	0.84[EUR][1000 genomes]
rs12090723	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12731675	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12731809	0.89[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	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1414367	0.81[EUR][1000 genomes]
rs1535698	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1535700	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1570528	0.92[EUR][1000 genomes]
rs2031223	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2031224	0.97[EUR][1000 genomes]
rs2104280	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2484485	0.81[EUR][1000 genomes]
rs2749735	0.82[EUR][1000 genomes]
rs2783492	0.82[EUR][1000 genomes]
rs2783498	0.84[EUR][1000 genomes]
rs2783506	0.82[EUR][1000 genomes]
rs2815408	0.81[EUR][1000 genomes]
rs2815409	0.81[EUR][1000 genomes]
rs2815410	0.82[EUR][1000 genomes]
rs2815411	0.82[EUR][1000 genomes]
rs2815412	0.81[EUR][1000 genomes]
rs2815413	0.83[EUR][1000 genomes]
rs2815414	0.85[EUR][1000 genomes]
rs4573531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4847239	0.88[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	0.97[EUR][1000 genomes]
rs4847411	0.87[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	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs504810	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505531	0.86[EUR][1000 genomes]
rs506556	0.84[EUR][1000 genomes]
rs508942	0.96[EUR][1000 genomes]
rs512361	0.97[EUR][1000 genomes]
rs519723	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs522999	0.83[EUR][1000 genomes]
rs523262	0.95[EUR][1000 genomes]
rs546	0.81[EUR][1000 genomes]
rs556888	0.97[EUR][1000 genomes]
rs558667	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56303209	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs566743	0.93[EUR][1000 genomes]
rs571212	0.89[EUR][1000 genomes]
rs573056	0.84[EUR][1000 genomes]
rs581825	0.83[EUR][1000 genomes]
rs587754	1.00[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	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs628714	0.95[EUR][1000 genomes]
rs629153	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs631966	0.97[EUR][1000 genomes]
rs633789	0.97[EUR][1000 genomes]
rs637198	0.96[EUR][1000 genomes]
rs641390	0.96[EUR][1000 genomes]
rs6541351	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6541400	0.97[EUR][1000 genomes]
rs658178	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs658877	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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667701	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	0.95[EUR][1000 genomes]
rs6701250	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	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	0.97[EUR][1000 genomes]
rs7525189	0.97[EUR][1000 genomes]
rs7529639	0.89[EUR][1000 genomes]
rs7546661	0.89[EUR][1000 genomes]
rs7551635	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7555292	0.92[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	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771459	0.89[EUR][1000 genomes]
rs771460	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771463	0.92[EUR][1000 genomes]
rs771464	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771466	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771467	0.90[EUR][1000 genomes]
rs771468	0.90[EUR][1000 genomes]
rs771469	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	0.90[EUR][1000 genomes]
rs771477	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	0.88[EUR][1000 genomes]
rs9432680	0.96[EUR][1000 genomes]
rs9432700	0.96[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	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
rs559397	RP4-717I23.3	cis	Artery Tibial	GTEx
rs559397	RP4-717I23.3	cis	Stomach	GTEx
rs559397	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs559397	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs559397	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs559397	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs559397	RP4-717I23.3	cis	Whole Blood	GTEx
rs559397	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs559397	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs559397	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs559397	RP4-717I23.3	cis	Thyroid	GTEx
rs559397	RP4-717I23.3	cis	lung	GTEx
rs559397	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs559397	RP4-717I23.3	cis	Artery Aorta	GTEx

Chromatin state (count:98 , 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	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
5	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
7	chr1:93720000-93762000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:93721200-93731400	Weak transcription	NH-A	brain
9	chr1:93724200-93731800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:93725200-93732600	Weak transcription	NHDF-Ad	bronchial
11	chr1:93726200-93729800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr1:93726400-93729800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:93726400-93730200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:93726400-93731600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:93726400-93731800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr1:93726400-93732000	Weak transcription	Right Ventricle	heart
17	chr1:93726600-93731800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr1:93726600-93731800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr1:93726800-93730000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr1:93726800-93730400	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr1:93726800-93731200	ZNF genes & repeats	GM12878-XiMat	blood
22	chr1:93726800-93731800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr1:93727000-93729200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
24	chr1:93727000-93729200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
25	chr1:93727000-93729600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr1:93727000-93729800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
27	chr1:93727000-93729800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr1:93727000-93729800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:93727000-93730000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
30	chr1:93727000-93730400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
31	chr1:93727000-93730400	Strong transcription	Fetal Lung	lung
32	chr1:93727000-93731200	ZNF genes & repeats	Dnd41	blood
33	chr1:93727000-93731800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:93727200-93729800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
35	chr1:93727400-93729800	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr1:93727600-93729400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
37	chr1:93727600-93730400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:93727800-93729800	Weak transcription	NHLF	lung
39	chr1:93727800-93731800	Weak transcription	NHEK	skin
40	chr1:93727800-93741600	Weak transcription	Fetal Kidney	kidney
41	chr1:93728400-93729200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:93728400-93730000	ZNF genes & repeats	Fetal Brain Female	brain
43	chr1:93728600-93729400	Weak transcription	Pancreas	Pancrea
44	chr1:93728600-93729800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:93728600-93730000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:93728600-93730200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:93728600-93731000	Strong transcription	A549	lung
48	chr1:93728600-93731600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:93728600-93738400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:93728600-93741000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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