Variant report

Variant	rs6759283
Chromosome Location	chr2:112967145-112967146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10864901	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11123133	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11676628	0.85[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11679986	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11682795	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11685462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11685514	0.93[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11687980	0.93[CEU][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11688511	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11689858	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11691239	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11693294	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11695974	0.93[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12474447	0.93[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12477879	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4516428	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55798617	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55802705	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55821286	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55861985	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56044884	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56048537	0.88[AMR][1000 genomes]
rs6711180	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6722612	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6747639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6761440	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831633	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831634	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831636	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831638	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831639	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72831641	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72831642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831649	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831651	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831658	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831660	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831662	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831664	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72831685	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72831688	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72833410	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833412	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833413	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833414	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833415	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833428	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72833431	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72833432	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7586893	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7587316	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7596661	0.93[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7599551	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6759283	RGPD8	cis	Nerve Tibial	GTEx
rs6759283	RGPD8	cis	Esophagus Mucosa	GTEx
rs6759283	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs6759283	RGPD8	cis	Artery Aorta	GTEx
rs6759283	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6759283	RGPD8	cis	Heart Left Ventricle	GTEx
rs6759283	FBLN7	cis	parietal	SCAN
rs6759283	RGPD8	cis	Artery Tibial	GTEx
rs6759283	RGPD8	cis	Adipose Subcutaneous	GTEx
rs6759283	RGPD8	cis	Esophagus Muscularis	GTEx
rs6759283	RGPD8	cis	Muscle Skeletal	GTEx
rs6759283	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6759283	RGPD8	cis	Thyroid	GTEx
rs6759283	RGPD8	cis	Whole Blood	GTEx
rs6759283	RGPD8	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:112945200-112970600	Weak transcription	Fetal Stomach	stomach
3	chr2:112959200-112969600	Weak transcription	Fetal Thymus	thymus
4	chr2:112959600-112987000	Weak transcription	Osteobl	bone
5	chr2:112961000-112968800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:112962400-112969000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:112962400-112969400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:112962400-112969800	Weak transcription	Liver	Liver
10	chr2:112962400-112979000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:112963200-112978800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:112964000-112973600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:112964800-112969600	Weak transcription	Fetal Brain Female	brain
14	chr2:112964800-112970400	Weak transcription	Dnd41	blood
15	chr2:112965000-112969400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:112965200-112972200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:112965400-112967200	Weak transcription	Aorta	Aorta
18	chr2:112965400-112969800	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:112965600-112969600	Weak transcription	Thymus	Thymus
20	chr2:112965600-112971600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:112965600-112972200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:112965800-112969200	Weak transcription	Primary B cells from cord blood	blood
23	chr2:112965800-112969600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:112965800-112971800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:112965800-112972000	Weak transcription	Lung	lung
26	chr2:112965800-112972200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:112966000-112968200	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:112966000-112969800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:112966200-112969600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:112966200-112969600	Weak transcription	Ovary	ovary
31	chr2:112966600-112968600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:112966600-112970400	Strong transcription	Primary T cells from cord blood	blood
33	chr2:112966600-112972200	Weak transcription	Brain Anterior Caudate	brain
34	chr2:112966800-112969600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:112967000-112969600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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