Variant report

Variant	rs34364366
Chromosome Location	chr2:113290878-113290879
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:113290591..113292898-chr2:113348416..113351140,2	K562	blood:
2	chr2:113289821..113291366-chr2:113297679..113299657,2	K562	blood:
3	chr2:113237305..113239187-chr2:113290058..113292165,2	K562	blood:
4	chr2:113290805..113292665-chr2:113298151..113300715,2	MCF-7	breast:
5	chr2:113289821..113292124-chr2:113297499..113299657,2	K562	blood:
6	chr2:113289491..113291465-chr2:113300196..113302655,2	K562	blood:
7	chr2:113284316..113286214-chr2:113288766..113291061,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11679929	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987434	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12988536	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	1.00[ASN][1000 genomes]
rs1465817	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561266	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047777	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6708841	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708927	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67178025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759275	1.00[ASN][1000 genomes]
rs71414672	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570679	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573493	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs34364366	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs34364366	RGPD8	cis	Muscle Skeletal	GTEx
rs34364366	RGPD8	cis	Esophagus Mucosa	GTEx
rs34364366	RGPD8	cis	Nerve Tibial	GTEx
rs34364366	RGPD8	cis	Adipose Subcutaneous	GTEx
rs34364366	RGPD8	cis	Whole Blood	GTEx
rs34364366	RGPD8	cis	Esophagus Muscularis	GTEx
rs34364366	RGPD8	cis	lung	GTEx
rs34364366	RGPD8	cis	Thyroid	GTEx
rs34364366	RGPD8	cis	Artery Aorta	GTEx
rs34364366	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs34364366	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs34364366	RGPD8	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
2	chr2:113260800-113298800	Weak transcription	Fetal Heart	heart
3	chr2:113270600-113298800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
5	chr2:113281200-113299000	Weak transcription	Colonic Mucosa	Colon
6	chr2:113284800-113291200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:113285600-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:113285800-113291200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:113285800-113291200	Strong transcription	Fetal Muscle Leg	muscle
10	chr2:113285800-113291200	Strong transcription	Thymus	Thymus
11	chr2:113285800-113291200	Strong transcription	Osteobl	bone
12	chr2:113285800-113291400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:113285800-113291400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:113285800-113291400	Strong transcription	Dnd41	blood
15	chr2:113285800-113291600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:113285800-113291600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:113286000-113291000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:113286000-113291200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:113286000-113291400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:113286000-113291400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:113286000-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:113286000-113291400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:113286000-113291400	Strong transcription	Fetal Thymus	thymus
24	chr2:113286000-113291400	Strong transcription	Left Ventricle	heart
25	chr2:113286000-113291600	Strong transcription	Fetal Stomach	stomach
26	chr2:113286000-113291600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:113286000-113292200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:113286000-113292200	Strong transcription	Fetal Brain Female	brain
29	chr2:113286200-113291000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:113286200-113291200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:113286200-113291200	Strong transcription	Adipose Nuclei	Adipose
32	chr2:113286200-113291200	Strong transcription	NHEK	skin
33	chr2:113286200-113291400	Strong transcription	HSMMtube	muscle
34	chr2:113286200-113291600	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr2:113286200-113291600	Strong transcription	HSMM	muscle
36	chr2:113286200-113292200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:113286400-113291000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:113286400-113291000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:113287000-113291200	Strong transcription	Lung	lung
40	chr2:113287000-113291400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:113287000-113291400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:113287000-113291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:113287000-113298800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:113287000-113298800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:113287000-113299000	Weak transcription	Fetal Intestine Small	intestine
46	chr2:113287000-113299000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:113287200-113298800	Weak transcription	Fetal Brain Male	brain
48	chr2:113287200-113298800	Weak transcription	Pancreas	Pancrea
49	chr2:113287200-113299000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:113287400-113298800	Weak transcription	Hela-S3	cervix

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