Variant report

Variant	rs55798617
Chromosome Location	chr2:112983874-112983875
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10864901	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123133	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11676628	0.86[EUR][1000 genomes]
rs11679986	0.95[EUR][1000 genomes]
rs11682795	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11685462	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11685514	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11687980	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11688511	0.85[EUR][1000 genomes]
rs11689858	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11691239	0.86[EUR][1000 genomes]
rs11693294	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11695974	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12474447	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12477879	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4516428	0.87[EUR][1000 genomes]
rs55802705	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55821286	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55861985	0.97[EUR][1000 genomes]
rs56044884	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56048537	0.83[EUR][1000 genomes]
rs6709304	0.94[AFR][1000 genomes]
rs6711180	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6722612	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6725166	0.88[AFR][1000 genomes]
rs6734458	0.94[AFR][1000 genomes]
rs6747097	0.83[AFR][1000 genomes]
rs6747639	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6757750	0.94[AFR][1000 genomes]
rs6759283	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6761440	0.86[EUR][1000 genomes]
rs72831633	0.86[EUR][1000 genomes]
rs72831634	0.86[EUR][1000 genomes]
rs72831636	0.86[EUR][1000 genomes]
rs72831638	0.86[EUR][1000 genomes]
rs72831639	0.83[EUR][1000 genomes]
rs72831641	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72831642	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72831649	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831651	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831658	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831660	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831662	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831664	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72831685	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72831688	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72833410	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833412	0.87[EUR][1000 genomes]
rs72833413	0.87[EUR][1000 genomes]
rs72833414	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833415	0.87[EUR][1000 genomes]
rs72833428	0.85[EUR][1000 genomes]
rs72833431	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72833432	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7586893	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7587316	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7596661	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7599551	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604747	0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs55798617	RGPD8	cis	Muscle Skeletal	GTEx
rs55798617	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs55798617	RGPD8	cis	Artery Aorta	GTEx
rs55798617	RGPD8	cis	Nerve Tibial	GTEx
rs55798617	RGPD8	cis	Adipose Subcutaneous	GTEx
rs55798617	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs55798617	RGPD8	cis	Thyroid	GTEx
rs55798617	RGPD8	cis	Artery Tibial	GTEx
rs55798617	RGPD8	cis	Esophagus Muscularis	GTEx
rs55798617	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs55798617	RGPD8	cis	lung	GTEx
rs55798617	RGPD8	cis	Esophagus Mucosa	GTEx
rs55798617	RGPD8	cis	Heart Left Ventricle	GTEx
rs55798617	RGPD8	cis	Whole Blood	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112959600-112987000	Weak transcription	Osteobl	bone
2	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:112967800-112986600	Weak transcription	NHEK	skin
4	chr2:112967800-112987000	Weak transcription	Aorta	Aorta
5	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
6	chr2:112968200-112999000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:112968200-113004000	Weak transcription	Fetal Brain Male	brain
8	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
9	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
10	chr2:112968400-112986800	Weak transcription	NHDF-Ad	bronchial
11	chr2:112968400-113003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
13	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:112969000-112993000	Weak transcription	Colonic Mucosa	Colon
15	chr2:112969000-113005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:112969200-112992000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
18	chr2:112969600-113009000	Weak transcription	Psoas Muscle	Psoas
19	chr2:112970200-112987600	Weak transcription	Adipose Nuclei	Adipose
20	chr2:112970200-112992600	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:112970200-113004800	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:112970800-113003800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:112970800-113005200	Weak transcription	Gastric	stomach
24	chr2:112970800-113011600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:112971400-113011600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:112971800-113011800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:112973000-112987200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:112973800-112986400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:112973800-112993000	Weak transcription	HepG2	liver
30	chr2:112974000-112986600	Weak transcription	HMEC	breast
31	chr2:112974000-112987000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:112974000-112990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:112974000-112993800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:112974000-112993800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:112974000-112993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:112974000-112994000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:112974000-113003600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:112974000-113004000	Weak transcription	Brain Anterior Caudate	brain
39	chr2:112974200-112993000	Weak transcription	Left Ventricle	heart
40	chr2:112975800-112986400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:112978200-113006400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:112979000-113004400	Weak transcription	Lung	lung
43	chr2:112979600-113003200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:112979600-113004000	Weak transcription	Fetal Heart	heart
45	chr2:112979600-113011600	Weak transcription	Fetal Kidney	kidney
46	chr2:112979600-113012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:112979800-112992600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:112980000-112984600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:112980000-112988000	Weak transcription	Brain Germinal Matrix	brain
50	chr2:112980000-112991600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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