Variant report

Variant	rs72831658
Chromosome Location	chr2:112995728-112995729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112993562..112995821-chr2:113031354..113033224,2	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10864901	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11123133	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11676628	0.87[EUR][1000 genomes]
rs11679986	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11682795	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11685462	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11685514	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11687980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11688511	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11689858	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11691239	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11693294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11695974	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12474447	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12477879	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4516428	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55798617	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55802705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55821286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55861985	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56044884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56048537	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6711180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6722612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6747639	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6759283	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6761440	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831633	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831634	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831636	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831638	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831639	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831641	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831642	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831662	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831664	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831685	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833412	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833413	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833414	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833415	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833428	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833431	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833432	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586893	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7587316	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7596661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7599551	0.96[AMR][1000 genomes];0.98[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	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs72831658	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs72831658	ZC3H8	cis	Artery Tibial	GTEx
rs72831658	RGPD8	cis	Thyroid	GTEx
rs72831658	RGPD8	cis	Adipose Subcutaneous	GTEx
rs72831658	RGPD8	cis	Muscle Skeletal	GTEx
rs72831658	RGPD8	cis	Whole Blood	GTEx
rs72831658	RGPD8	cis	Esophagus Mucosa	GTEx
rs72831658	RGPD8	cis	lung	GTEx
rs72831658	RGPD8	cis	Heart Left Ventricle	GTEx
rs72831658	RGPD8	cis	Esophagus Muscularis	GTEx
rs72831658	RGPD8	cis	Artery Aorta	GTEx
rs72831658	RGPD8	cis	Nerve Tibial	GTEx
rs72831658	RGPD8	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
3	chr2:112968200-112999000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:112968200-113004000	Weak transcription	Fetal Brain Male	brain
5	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
6	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
7	chr2:112968400-113003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:112969000-113005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
12	chr2:112969600-113009000	Weak transcription	Psoas Muscle	Psoas
13	chr2:112970200-113004800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:112970800-113003800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:112970800-113005200	Weak transcription	Gastric	stomach
16	chr2:112970800-113011600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:112971400-113011600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:112971800-113011800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:112974000-113003600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:112974000-113004000	Weak transcription	Brain Anterior Caudate	brain
21	chr2:112978200-113006400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:112979000-113004400	Weak transcription	Lung	lung
23	chr2:112979600-113003200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:112979600-113004000	Weak transcription	Fetal Heart	heart
25	chr2:112979600-113011600	Weak transcription	Fetal Kidney	kidney
26	chr2:112979600-113012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:112980000-113002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:112980000-113003000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:112980000-113003600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:112980000-113004600	Weak transcription	Placenta	Placenta
31	chr2:112980000-113005400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:112980000-113011800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:112980200-112999800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:112980200-113003200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:112980200-113011600	Weak transcription	HSMM	muscle
36	chr2:112980400-113003200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:112982400-113000200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:112985200-112998800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:112985200-113003400	Weak transcription	Fetal Brain Female	brain
40	chr2:112986000-113003000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:112987200-113003600	Weak transcription	GM12878-XiMat	blood
42	chr2:112987200-113004000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:112987200-113010800	Weak transcription	NH-A	brain
44	chr2:112987200-113011000	Weak transcription	NHDF-Ad	bronchial
45	chr2:112987400-113002200	Weak transcription	Osteobl	bone
46	chr2:112987400-113005600	Weak transcription	Aorta	Aorta
47	chr2:112987400-113011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:112987800-113011000	Weak transcription	NHEK	skin
49	chr2:112987800-113011800	Weak transcription	NHLF	lung
50	chr2:112988400-113011600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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