Variant report

Variant	rs712663
Chromosome Location	chr5:112223594-112223595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112199613..112201992-chr5:112222873..112225577,2	K562	blood:
2	chr5:112211665..112213695-chr5:112223485..112225532,2	K562	blood:
3	chr5:112221269..112223827-chr5:112227698..112230274,2	K562	blood:
4	chr5:112223124..112224717-chr5:112225573..112227485,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153037	Chromatin interaction
ENSG00000270067	Chromatin interaction
ENSG00000212643	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1069061	0.87[EUR][1000 genomes]
rs1093611	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1093677	0.86[EUR][1000 genomes]
rs149193	0.84[ASN][1000 genomes]
rs151976	0.85[EUR][1000 genomes]
rs151977	0.85[EUR][1000 genomes]
rs151978	0.85[EUR][1000 genomes]
rs153544	0.85[ASN][1000 genomes]
rs153546	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153548	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153549	0.94[ASN][1000 genomes]
rs153550	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153551	0.94[ASN][1000 genomes]
rs153552	0.92[ASN][1000 genomes]
rs153558	0.81[EUR][1000 genomes]
rs153565	0.82[AMR][1000 genomes]
rs154344	0.85[ASN][1000 genomes]
rs2545156	0.95[ASN][1000 genomes]
rs2545166	0.86[EUR][1000 genomes]
rs2545167	0.86[EUR][1000 genomes]
rs2545170	0.91[ASN][1000 genomes]
rs2546112	0.83[ASN][1000 genomes]
rs2546115	0.86[ASN][1000 genomes]
rs2909904	0.85[EUR][1000 genomes]
rs3317	0.92[ASN][1000 genomes]
rs351767	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351768	0.95[ASN][1000 genomes]
rs351769	0.83[EUR][1000 genomes]
rs351770	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35726351	0.87[EUR][1000 genomes]
rs368575	0.92[ASN][1000 genomes]
rs372492	0.83[EUR][1000 genomes]
rs373059	0.80[ASN][1000 genomes]
rs374613	0.86[ASN][1000 genomes]
rs380144	0.80[EUR][1000 genomes]
rs382260	0.86[EUR][1000 genomes]
rs382427	0.84[ASN][1000 genomes]
rs395858	0.84[ASN][1000 genomes]
rs410701	0.91[ASN][1000 genomes]
rs41116	0.82[ASN][1000 genomes]
rs419155	0.92[ASN][1000 genomes]
rs419632	0.87[EUR][1000 genomes]
rs430665	0.96[EUR][1000 genomes]
rs431287	0.83[EUR][1000 genomes]
rs434090	0.82[EUR][1000 genomes]
rs438252	0.84[EUR][1000 genomes]
rs439456	0.93[EUR][1000 genomes]
rs446567	0.83[EUR][1000 genomes]
rs448162	0.84[ASN][1000 genomes]
rs448475	0.82[ASN][1000 genomes]
rs448613	0.92[ASN][1000 genomes]
rs454968	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs455412	0.96[EUR][1000 genomes]
rs455469	0.81[EUR][1000 genomes]
rs456313	0.88[EUR][1000 genomes]
rs456531	0.94[ASN][1000 genomes]
rs458451	0.96[EUR][1000 genomes]
rs459102	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs460137	0.84[ASN][1000 genomes]
rs460301	0.86[EUR][1000 genomes]
rs460832	0.96[EUR][1000 genomes]
rs461424	0.83[EUR][1000 genomes]
rs461866	0.89[EUR][1000 genomes]
rs463229	0.84[EUR][1000 genomes]
rs465454	0.85[EUR][1000 genomes]
rs468101	0.88[EUR][1000 genomes]
rs468610	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs468751	0.85[ASN][1000 genomes]
rs468783	0.82[EUR][1000 genomes]
rs468854	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs469663	0.92[EUR][1000 genomes]
rs469727	0.90[EUR][1000 genomes]
rs469760	0.82[EUR][1000 genomes]
rs469827	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469886	0.87[ASN][1000 genomes]
rs481789	0.80[EUR][1000 genomes]
rs495794	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs497844	0.80[EUR][1000 genomes]
rs505382	0.86[ASN][1000 genomes]
rs514763	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519397	0.84[EUR][1000 genomes]
rs565453	0.80[EUR][1000 genomes]
rs565603	0.80[EUR][1000 genomes]
rs566419	0.85[ASN][1000 genomes]
rs580237	0.80[EUR][1000 genomes]
rs67293732	0.94[ASN][1000 genomes]
rs698405	0.92[EUR][1000 genomes]
rs712662	0.96[EUR][1000 genomes]
rs712664	0.91[EUR][1000 genomes]
rs712665	0.96[EUR][1000 genomes]
rs712666	0.94[EUR][1000 genomes]
rs712668	0.83[EUR][1000 genomes]
rs712670	0.92[ASN][1000 genomes]
rs712671	0.94[EUR][1000 genomes]
rs7213	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs818423	0.87[EUR][1000 genomes]
rs818424	0.92[EUR][1000 genomes]
rs818425	0.88[EUR][1000 genomes]
rs818427	0.87[EUR][1000 genomes]
rs818428	0.95[ASN][1000 genomes]
rs818429	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs818430	0.95[ASN][1000 genomes]
rs818797	0.95[ASN][1000 genomes]
rs864682	0.88[EUR][1000 genomes]
rs9011	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv3470639	chr5:112222353-112227151	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	esv3451617	chr5:112223580-112223920	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs712663	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs712663	REEP5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
4	chr5:112208200-112225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:112209600-112225000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:112209600-112226400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:112209800-112224600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:112210600-112225000	Strong transcription	Liver	Liver
11	chr5:112210800-112225000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr5:112211200-112240000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:112211800-112239200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:112212400-112225200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:112212400-112225400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:112212600-112251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:112213000-112224600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:112213200-112229400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:112213800-112225000	Strong transcription	Fetal Intestine Large	intestine
23	chr5:112214000-112224400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:112214200-112232200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:112214800-112226600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:112214800-112234800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr5:112215200-112224800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:112215200-112255800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:112215800-112223600	Strong transcription	NHEK	skin
30	chr5:112215800-112224800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:112215800-112225400	Strong transcription	GM12878-XiMat	blood
32	chr5:112215800-112226000	Strong transcription	A549	lung
33	chr5:112215800-112240400	Strong transcription	Primary B cells from cord blood	blood
34	chr5:112215800-112247200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:112216000-112225000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:112216400-112226800	Strong transcription	Dnd41	blood
37	chr5:112217000-112223600	Strong transcription	HSMM	muscle
38	chr5:112217000-112223600	Strong transcription	NHDF-Ad	bronchial
39	chr5:112217400-112223600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:112219800-112232200	Strong transcription	Fetal Intestine Small	intestine
41	chr5:112220000-112224400	Weak transcription	Right Atrium	heart
42	chr5:112221400-112237800	Weak transcription	Small Intestine	intestine
43	chr5:112221800-112225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:112221800-112231400	Weak transcription	Psoas Muscle	Psoas
45	chr5:112221800-112231800	Weak transcription	Stomach Mucosa	stomach
46	chr5:112221800-112256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:112222000-112231400	Weak transcription	Hela-S3	cervix
48	chr5:112222000-112233800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:112222000-112256400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:112222200-112229200	Weak transcription	H1 Cell Line	embryonic stem cell

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