Variant report

Variant	rs6722612
Chromosome Location	chr2:113016736-113016737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:113016689-113017971	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr2:113016629-113017619	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr2:113016592-113018003	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113013729..113015547-chr2:113015611..113017197,2	K562	blood:
2	chr2:113015323..113017823-chr2:113341414..113343935,3	K562	blood:
3	chr2:113012803..113017644-chr2:113018976..113023020,5	K562	blood:
4	chr2:113009620..113015521-chr2:113015637..113020562,9	K562	blood:
5	chr2:113016144..113018548-chr2:113019194..113021994,2	K562	blood:
6	chr2:113015328..113018702-chr2:113341013..113343935,4	K562	blood:
7	chr2:112813000..112815261-chr2:113015574..113017538,2	K562	blood:

No data

Variant related genes	Relation type
ZC3H8	TF binding region
ENSG00000153214	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000144161	Chromatin interaction

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

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];0.97[EUR][1000 genomes]
rs11676628	0.87[EUR][1000 genomes]
rs11679986	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11682795	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11685462	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11685514	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11687980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11688511	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11689858	1.00[AMR][1000 genomes];1.00[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];0.98[EUR][1000 genomes]
rs11695974	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12474447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12477879	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4516428	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55798617	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55802705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55821286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55861985	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56044884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048537	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6711180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6747639	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6759283	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6761440	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[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];0.84[EUR][1000 genomes]
rs72831641	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72831642	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831651	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831662	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831664	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831685	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72833410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833412	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833413	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833414	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833415	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833428	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72833431	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72833432	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7586893	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7587316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7596661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7599551	0.96[AMR][1000 genomes];0.97[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6722612	ZC3H8	cis	Artery Tibial	GTEx
rs6722612	RGPD8	cis	Nerve Tibial	GTEx
rs6722612	RGPD8	cis	Muscle Skeletal	GTEx
rs6722612	RGPD8	cis	lung	GTEx
rs6722612	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs6722612	RGPD8	cis	Esophagus Mucosa	GTEx
rs6722612	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6722612	RGPD8	cis	Artery Aorta	GTEx
rs6722612	RGPD8	cis	Heart Left Ventricle	GTEx
rs6722612	RGPD8	cis	Thyroid	GTEx
rs6722612	RGPD8	cis	Artery Tibial	GTEx
rs6722612	RGPD8	cis	Adipose Subcutaneous	GTEx
rs6722612	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6722612	RGPD8	cis	Esophagus Muscularis	GTEx
rs6722612	RGPD8	cis	Whole Blood	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113012600-113016800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:113012600-113016800	Weak transcription	Fetal Heart	heart
3	chr2:113012600-113017200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113012800-113017000	Weak transcription	Spleen	Spleen
5	chr2:113012800-113017200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:113013000-113016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:113013000-113016800	Weak transcription	Fetal Kidney	kidney
8	chr2:113013000-113017000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:113013000-113017000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:113013000-113017000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:113013000-113017000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:113013000-113017000	Weak transcription	Fetal Lung	lung
13	chr2:113013000-113017000	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:113013000-113017000	Weak transcription	Psoas Muscle	Psoas
15	chr2:113013000-113017000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:113013000-113017000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:113013000-113017000	Weak transcription	HMEC	breast
18	chr2:113013000-113017000	Weak transcription	NH-A	brain
19	chr2:113013000-113017000	Weak transcription	NHDF-Ad	bronchial
20	chr2:113013000-113017000	Weak transcription	NHEK	skin
21	chr2:113013000-113017000	Weak transcription	NHLF	lung
22	chr2:113013000-113017200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:113013000-113017200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:113013000-113017200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:113013000-113017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:113013000-113017200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:113013000-113017200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:113013000-113017200	Weak transcription	Pancreas	Pancrea
29	chr2:113013000-113017400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:113013000-113018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:113013000-113018200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:113013200-113016800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:113013200-113016800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:113013200-113016800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:113013200-113017000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:113013200-113017000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:113013200-113017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:113013200-113017000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:113013200-113017000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:113013200-113017000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:113013200-113017000	Weak transcription	Liver	Liver
42	chr2:113013200-113017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:113013200-113017000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:113013200-113017000	Weak transcription	Left Ventricle	heart
45	chr2:113013200-113017000	Weak transcription	Ovary	ovary
46	chr2:113013200-113017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:113013200-113017200	Weak transcription	Hela-S3	cervix
48	chr2:113013400-113016800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:113013400-113016800	Weak transcription	Brain Anterior Caudate	brain
50	chr2:113013400-113016800	Weak transcription	Brain Inferior Temporal Lobe	brain

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