Variant report

Variant	rs72831685
Chromosome Location	chr2:113036555-113036556
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113031252..113036924-chr2:113235926..113242226,12	K562	blood:
2	chr2:113031538..113036695-chr2:113297613..113301921,6	K562	blood:

Variant related genes	Relation type
ENSG00000114999	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10864901	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11123133	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11676628	0.86[EUR][1000 genomes]
rs11679986	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11682795	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11685462	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11685514	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11687980	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11688511	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11689858	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11691239	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11693294	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11695974	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12474447	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12477879	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4516428	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55798617	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55802705	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55821286	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55861985	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56044884	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56048537	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6711180	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6722612	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6747639	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6759283	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6761440	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831633	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831634	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831636	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831638	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831639	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72831641	0.88[EUR][1000 genomes]
rs72831642	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72831649	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831651	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831658	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831660	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831662	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831664	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72831688	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833410	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833412	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833413	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833414	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833415	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833428	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833431	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833432	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7586893	0.84[EUR][1000 genomes]
rs7587316	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7596661	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7599551	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
6	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
7	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
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv874872	chr2:113027569-113070889	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv963704	chr2:113036252-113044944	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs72831685	RGPD8	cis	Heart Left Ventricle	GTEx
rs72831685	RGPD8	cis	Artery Aorta	GTEx
rs72831685	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs72831685	RGPD8	cis	Whole Blood	GTEx
rs72831685	RGPD8	cis	Artery Tibial	GTEx
rs72831685	RGPD8	cis	Adipose Subcutaneous	GTEx
rs72831685	ZC3H8	cis	Artery Tibial	GTEx
rs72831685	RGPD8	cis	Esophagus Mucosa	GTEx
rs72831685	RGPD8	cis	Esophagus Muscularis	GTEx
rs72831685	RGPD8	cis	lung	GTEx
rs72831685	RGPD8	cis	Nerve Tibial	GTEx
rs72831685	RGPD8	cis	Muscle Skeletal	GTEx
rs72831685	RGPD8	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034200-113058200	Weak transcription	Ovary	ovary
2	chr2:113034400-113036600	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr2:113034400-113047800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:113034400-113051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
6	chr2:113034600-113037400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:113034600-113039600	Weak transcription	Fetal Heart	heart
8	chr2:113034800-113037000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:113034800-113039600	Weak transcription	HepG2	liver
10	chr2:113034800-113041400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:113035000-113036600	Enhancers	Liver	Liver
12	chr2:113035000-113046000	Weak transcription	Fetal Kidney	kidney
13	chr2:113035000-113057800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:113035000-113057800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:113035000-113057800	Weak transcription	Fetal Intestine Small	intestine
16	chr2:113035200-113040200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:113035400-113036600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:113035400-113037000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:113035400-113040600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:113035400-113047600	Weak transcription	Osteobl	bone
21	chr2:113035600-113036800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:113035600-113040400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:113035600-113041200	Weak transcription	K562	blood
24	chr2:113035600-113047600	Weak transcription	NHDF-Ad	bronchial
25	chr2:113035600-113058200	Weak transcription	Primary B cells from cord blood	blood
26	chr2:113035800-113036600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr2:113035800-113038000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:113035800-113040200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:113035800-113058000	Weak transcription	Primary T cells from cord blood	blood
30	chr2:113035800-113060400	Weak transcription	Fetal Thymus	thymus
31	chr2:113035800-113067400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:113036000-113040000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:113036000-113040000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:113036000-113040600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:113036200-113041200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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