Variant report

Variant	rs13166089
Chromosome Location	chr5:76098215-76098216
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10053003	0.83[ASN][1000 genomes]
rs1030484	0.86[ASN][1000 genomes]
rs12186639	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs13157422	0.87[ASN][1000 genomes]
rs13166450	0.86[ASN][1000 genomes]
rs13177258	0.87[ASN][1000 genomes]
rs13179180	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13179405	0.90[ASN][1000 genomes]
rs13180705	0.81[ASN][1000 genomes]
rs166175	0.83[AMR][1000 genomes]
rs185156	0.83[AMR][1000 genomes]
rs1963861	0.84[ASN][1000 genomes]
rs2243010	0.94[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2434656	0.88[ASN][1000 genomes]
rs250755	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs250756	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs250763	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs250764	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135471	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34469953	0.88[ASN][1000 genomes]
rs3925483	0.89[ASN][1000 genomes]
rs429332	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs458380	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704366	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs55925929	0.91[ASN][1000 genomes]
rs56238109	0.81[ASN][1000 genomes]
rs62365101	0.85[ASN][1000 genomes]
rs62365102	0.81[ASN][1000 genomes]
rs62365104	0.87[ASN][1000 genomes]
rs62365105	0.87[ASN][1000 genomes]
rs6453253	0.82[ASN][1000 genomes]
rs7712660	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv462213	chr5:76067624-76112869	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv598682	chr5:76067624-76112869	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1015997	chr5:76079720-76129241	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1031491	chr5:76083382-76129241	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2763908	chr5:76083394-76134777	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv598683	chr5:76086597-76129053	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv882210	chr5:76086597-76140337	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1022431	chr5:76086795-76127170	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1020397	chr5:76086795-76129241	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv598684	chr5:76086795-76130113	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1025151	chr5:76086795-76134777	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025061	chr5:76087544-76129241	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1033086	chr5:76088861-76129241	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1021460	chr5:76089512-76129241	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1018194	chr5:76090951-76129241	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv521533	chr5:76092225-76100536	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv598685	chr5:76092225-76128521	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13166089	F2RL1	cis	parietal	SCAN
rs13166089	F2R	cis	Muscle Skeletal	GTEx
rs13166089	F2RL1	cis	multi-tissue	Pritchard
rs13166089	DMGDH	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76088000-76100000	Weak transcription	HepG2	liver
2	chr5:76088200-76101400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:76091000-76101800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:76095000-76101400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:76095400-76099800	Weak transcription	Fetal Intestine Small	intestine
6	chr5:76097400-76100000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:76097400-76101400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:76097400-76101600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:76097600-76100000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:76097600-76101400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:76097800-76099800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:76097800-76100400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:76097800-76101400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:76097800-76101400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:76097800-76101400	Weak transcription	NHDF-Ad	bronchial
16	chr5:76097800-76101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:76098000-76099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:76098000-76099800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:76098000-76099800	Weak transcription	NH-A	brain
20	chr5:76098000-76100000	Enhancers	A549	lung
21	chr5:76098000-76100000	Weak transcription	Osteobl	bone
22	chr5:76098000-76100200	Weak transcription	HUVEC	blood vessel
23	chr5:76098000-76101400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:76098000-76101400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:76098000-76101400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:76098000-76101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:76098000-76101400	Weak transcription	Hela-S3	cervix
28	chr5:76098000-76101400	Weak transcription	HSMMtube	muscle
29	chr5:76098000-76101400	Weak transcription	NHEK	skin
30	chr5:76098000-76101400	Weak transcription	NHLF	lung
31	chr5:76098000-76101600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:76098000-76104000	Weak transcription	Spleen	Spleen
33	chr5:76098000-76105000	Weak transcription	Right Atrium	heart
34	chr5:76098200-76101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:76098200-76101600	Weak transcription	HMEC	breast

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