Variant report

Variant	rs34179430
Chromosome Location	chr2:113259739-113259740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10169344	0.81[JPT][hapmap]
rs10205187	0.81[JPT][hapmap]
rs11692276	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12464735	0.94[ASN][1000 genomes]
rs12469608	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13024583	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395691	0.81[JPT][hapmap]
rs13395779	0.81[JPT][hapmap]
rs13412193	0.81[JPT][hapmap]
rs1583616	0.81[JPT][hapmap]
rs3789724	0.81[JPT][hapmap]
rs57492581	0.93[ASN][1000 genomes]
rs62157497	0.94[ASN][1000 genomes]
rs62157498	0.94[ASN][1000 genomes]
rs62157536	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7559710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7576952	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7601108	0.94[ASN][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs34179430	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs34179430	RGPD8	cis	lung	GTEx
rs34179430	FBLN7	cis	parietal	SCAN
rs34179430	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs34179430	RGPD8	cis	Adipose Subcutaneous	GTEx
rs34179430	RGPD8	cis	Artery Tibial	GTEx
rs34179430	RGPD8	cis	Thyroid	GTEx
rs34179430	RGPD8	cis	Muscle Skeletal	GTEx
rs34179430	POLR1B	cis	cerebellum	SCAN
rs34179430	RGPD8	cis	Nerve Tibial	GTEx
rs34179430	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr2:113241600-113260600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
11	chr2:113241800-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:113245800-113277200	Weak transcription	Right Ventricle	heart
14	chr2:113245800-113277200	Weak transcription	Spleen	Spleen
15	chr2:113246200-113271600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:113252000-113271600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:113252000-113277800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:113252200-113271800	Weak transcription	Hela-S3	cervix
19	chr2:113252200-113272200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:113252200-113276600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:113252200-113277800	Weak transcription	Psoas Muscle	Psoas
22	chr2:113252800-113277200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:113253000-113259800	Weak transcription	NHDF-Ad	bronchial
24	chr2:113253000-113272200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:113253000-113272200	Weak transcription	Fetal Kidney	kidney
26	chr2:113253000-113277000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:113253000-113277000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:113253000-113277800	Weak transcription	Brain Substantia Nigra	brain
29	chr2:113253200-113260200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:113253200-113260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:113253200-113260400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:113253200-113266800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr2:113253200-113271800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:113253200-113272400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:113253200-113272800	Weak transcription	Fetal Intestine Large	intestine
36	chr2:113253200-113277000	Weak transcription	Lung	lung
37	chr2:113253200-113277200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:113253400-113277800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:113253600-113259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:113253600-113259800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:113253600-113272200	Weak transcription	Primary T cells from cord blood	blood
42	chr2:113253600-113272600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:113253600-113276800	Weak transcription	HSMMtube	muscle
44	chr2:113253800-113267200	Weak transcription	K562	blood
45	chr2:113253800-113272200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:113253800-113275400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:113253800-113277800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:113254200-113267200	Weak transcription	HepG2	liver
49	chr2:113258600-113260000	Strong transcription	Fetal Stomach	stomach
50	chr2:113258600-113260400	Strong transcription	Dnd41	blood

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