Variant report

Variant	rs11679929
Chromosome Location	chr2:113256350-113256351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113249787..113252523-chr2:113253686..113256564,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12987434	1.00[ASN][1000 genomes]
rs12988536	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	1.00[ASN][1000 genomes]
rs1465817	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561266	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047777	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34364366	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6707618	0.87[EUR][1000 genomes]
rs6708841	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708927	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67178025	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759275	1.00[ASN][1000 genomes]
rs71414672	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414673	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570679	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573493	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	0.91[AMR][1000 genomes];0.96[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
rs11679929	RGPD8	cis	Thyroid	GTEx
rs11679929	RGPD8	cis	Artery Tibial	GTEx
rs11679929	RGPD8	cis	Whole Blood	GTEx
rs11679929	RGPD8	cis	Esophagus Mucosa	GTEx
rs11679929	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs11679929	RGPD8	cis	Esophagus Muscularis	GTEx
rs11679929	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs11679929	RGPD8	cis	Nerve Tibial	GTEx
rs11679929	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs11679929	RGPD8	cis	lung	GTEx
rs11679929	RGPD8	cis	Adipose Subcutaneous	GTEx
rs11679929	RGPD8	cis	Artery Aorta	GTEx
rs11679929	RGPD8	cis	Muscle Skeletal	GTEx

Chromatin state (count:119 , 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	chr2:113241200-113259600	Weak transcription	Esophagus	oesophagus
4	chr2:113241200-113271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:113241200-113277800	Weak transcription	Pancreas	Pancrea
6	chr2:113241200-113278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:113241400-113279200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:113241600-113260600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
12	chr2:113241800-113257800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:113241800-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:113242000-113259600	Weak transcription	Fetal Heart	heart
16	chr2:113244800-113259600	Weak transcription	GM12878-XiMat	blood
17	chr2:113245800-113277200	Weak transcription	Right Ventricle	heart
18	chr2:113245800-113277200	Weak transcription	Spleen	Spleen
19	chr2:113246200-113271600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:113251600-113259600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:113252000-113259600	Weak transcription	Placenta	Placenta
22	chr2:113252000-113259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:113252000-113271600	Weak transcription	Fetal Intestine Small	intestine
24	chr2:113252000-113277800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:113252200-113257000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:113252200-113259400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:113252200-113271800	Weak transcription	Hela-S3	cervix
28	chr2:113252200-113272200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:113252200-113276600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:113252200-113277800	Weak transcription	Psoas Muscle	Psoas
31	chr2:113252800-113277200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:113253000-113259400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:113253000-113259400	Weak transcription	HMEC	breast
34	chr2:113253000-113259600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:113253000-113259600	Weak transcription	Brain Anterior Caudate	brain
36	chr2:113253000-113259600	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:113253000-113259600	Weak transcription	Fetal Lung	lung
38	chr2:113253000-113259600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:113253000-113259600	Weak transcription	NHLF	lung
40	chr2:113253000-113259800	Weak transcription	NHDF-Ad	bronchial
41	chr2:113253000-113272200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr2:113253000-113272200	Weak transcription	Fetal Kidney	kidney
43	chr2:113253000-113277000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:113253000-113277000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:113253000-113277800	Weak transcription	Brain Substantia Nigra	brain
46	chr2:113253200-113259000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:113253200-113259400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:113253200-113259400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:113253200-113259400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:113253200-113259400	Weak transcription	Brain Inferior Temporal Lobe	brain

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