Variant report

Variant	rs7573493
Chromosome Location	chr2:113269901-113269902
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	chr2:113269592..113271917-chr2:113298456..113301388,2	MCF-7	breast:
2	chr2:113268955..113271079-chr2:113298018..113300061,2	K562	blood:

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:25)

rs_ID	r²[population]
rs11679929	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[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];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	1.00[ASN][1000 genomes]
rs1465817	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561266	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047777	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34364366	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6707618	0.85[EUR][1000 genomes]
rs6708841	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708927	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67178025	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759275	1.00[ASN][1000 genomes]
rs71414672	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414673	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570679	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7573493	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs7573493	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7573493	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7573493	RGPD8	cis	Artery Aorta	GTEx
rs7573493	RGPD8	cis	Thyroid	GTEx
rs7573493	RGPD8	cis	Adipose Subcutaneous	GTEx
rs7573493	RGPD8	cis	Esophagus Muscularis	GTEx
rs7573493	RGPD8	cis	Muscle Skeletal	GTEx
rs7573493	RGPD8	cis	Whole Blood	GTEx
rs7573493	RGPD8	cis	lung	GTEx
rs7573493	RGPD8	cis	Artery Tibial	GTEx
rs7573493	RGPD8	cis	Esophagus Mucosa	GTEx
rs7573493	RGPD8	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241000-113277200	Weak transcription	Gastric	stomach
2	chr2:113241000-113277800	Weak transcription	Colonic Mucosa	Colon
3	chr2:113241200-113271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:113241200-113277800	Weak transcription	Pancreas	Pancrea
5	chr2:113241200-113278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:113241400-113279200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
10	chr2:113241800-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:113245800-113277200	Weak transcription	Right Ventricle	heart
13	chr2:113245800-113277200	Weak transcription	Spleen	Spleen
14	chr2:113246200-113271600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:113252000-113271600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:113252000-113277800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:113252200-113271800	Weak transcription	Hela-S3	cervix
18	chr2:113252200-113272200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr2:113252200-113276600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:113252200-113277800	Weak transcription	Psoas Muscle	Psoas
21	chr2:113252800-113277200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:113253000-113272200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:113253000-113272200	Weak transcription	Fetal Kidney	kidney
24	chr2:113253000-113277000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:113253000-113277000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:113253000-113277800	Weak transcription	Brain Substantia Nigra	brain
27	chr2:113253200-113271800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:113253200-113272400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:113253200-113272800	Weak transcription	Fetal Intestine Large	intestine
30	chr2:113253200-113277000	Weak transcription	Lung	lung
31	chr2:113253200-113277200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:113253400-113277800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:113253600-113272200	Weak transcription	Primary T cells from cord blood	blood
34	chr2:113253600-113272600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:113253600-113276800	Weak transcription	HSMMtube	muscle
36	chr2:113253800-113272200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:113253800-113275400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:113253800-113277800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:113259800-113272000	Weak transcription	GM12878-XiMat	blood
40	chr2:113260000-113277000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:113260000-113277800	Weak transcription	Aorta	Aorta
42	chr2:113260200-113272200	Weak transcription	A549	lung
43	chr2:113260200-113277200	Weak transcription	Thymus	Thymus
44	chr2:113260600-113271600	Weak transcription	HUVEC	blood vessel
45	chr2:113260600-113277800	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:113260600-113278000	Weak transcription	Ovary	ovary
47	chr2:113260800-113270000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:113260800-113270600	Weak transcription	Adipose Nuclei	Adipose
49	chr2:113260800-113270800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:113260800-113270800	Weak transcription	NHDF-Ad	bronchial

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