Variant report

Variant	rs8076915
Chromosome Location	chr17:38391526-38391527
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1130199	0.92[ASW][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs12936565	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12937995	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12944531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12947188	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34789145	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7213066	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7218938	0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7224658	1.00[ASW][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8065665	1.00[ASW][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8066144	0.83[LWK][hapmap];0.91[MKK][hapmap]
rs8067148	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8072718	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8074251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9892367	0.92[ASW][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv522863	chr17:38388040-38405037	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv525961	chr17:38388040-38405037	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8076915	RAPGEFL1	cis	lymphoblastoid	seeQTL
rs8076915	RAPGEFL1	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38376600-38392200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:38376600-38393200	Weak transcription	Fetal Heart	heart
3	chr17:38376600-38400400	Weak transcription	Psoas Muscle	Psoas
4	chr17:38376600-38412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr17:38376600-38416800	Weak transcription	Aorta	Aorta
6	chr17:38376800-38391600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr17:38376800-38393600	Weak transcription	HMEC	breast
8	chr17:38377000-38418400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:38377200-38404800	Weak transcription	HSMMtube	muscle
10	chr17:38377400-38408000	Weak transcription	Small Intestine	intestine
11	chr17:38377600-38412800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr17:38377800-38400400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:38379200-38413000	Weak transcription	Pancreas	Pancrea
14	chr17:38381200-38391600	Weak transcription	Fetal Brain Male	brain
15	chr17:38381200-38412400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:38381400-38399000	Weak transcription	NHLF	lung
17	chr17:38381400-38407000	Weak transcription	Hela-S3	cervix
18	chr17:38381400-38407400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:38381400-38407400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr17:38381400-38407400	Weak transcription	Osteobl	bone
21	chr17:38381600-38397600	Weak transcription	Brain Substantia Nigra	brain
22	chr17:38381800-38407600	Weak transcription	K562	blood
23	chr17:38381800-38408000	Weak transcription	Right Ventricle	heart
24	chr17:38382000-38397400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:38382000-38397600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr17:38382000-38399200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:38382000-38407600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr17:38382000-38412400	Weak transcription	Fetal Lung	lung
29	chr17:38382800-38399400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:38385000-38392400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:38385400-38407600	Weak transcription	NHEK	skin
32	chr17:38386000-38393200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr17:38386000-38407800	Weak transcription	Adipose Nuclei	Adipose
34	chr17:38387400-38397400	Weak transcription	Brain Hippocampus Middle	brain
35	chr17:38387600-38396600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr17:38387600-38397600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr17:38387600-38400200	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:38387800-38393800	Strong transcription	Fetal Stomach	stomach
39	chr17:38387800-38394000	Strong transcription	Fetal Intestine Small	intestine
40	chr17:38388400-38394600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr17:38388600-38391800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:38388600-38391800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:38388600-38392000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr17:38388600-38392800	Strong transcription	Fetal Intestine Large	intestine
45	chr17:38388600-38392800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr17:38388600-38393800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr17:38388600-38394000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr17:38388600-38394000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:38388600-38398000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:38389000-38393800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links