Variant report

Variant	rs7706217
Chromosome Location	chr5:114573873-114573874
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10045548	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10059069	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10076833	0.81[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes]
rs10079380	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11745083	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11745170	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11960213	0.85[ASN][1000 genomes]
rs17640052	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2053697	0.81[EUR][1000 genomes]
rs2303001	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs265417	0.91[ASN][1000 genomes]
rs265437	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs267297	0.81[CEU][hapmap]
rs267298	0.81[CEU][hapmap]
rs3805580	0.96[CEU][hapmap];0.90[YRI][hapmap];0.95[EUR][1000 genomes]
rs3805581	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3805586	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs62383165	0.96[ASN][1000 genomes]
rs6594883	0.92[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs67276221	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6878733	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6884828	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6886102	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7725831	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9326954	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.97[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	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1029371	chr5:114541428-114590891	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7706217	PGGT1B	cis	multi-tissue	Pritchard
rs7706217	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs7706217	PGGT1B	cis	normal skin	skin_eQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
2	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
3	chr5:114539200-114580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:114542000-114575800	Weak transcription	Small Intestine	intestine
5	chr5:114543800-114577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:114546800-114575600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:114546800-114578000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:114547600-114577600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:114547800-114578400	Weak transcription	Esophagus	oesophagus
10	chr5:114547800-114596600	Weak transcription	Brain Germinal Matrix	brain
11	chr5:114548400-114596800	Weak transcription	K562	blood
12	chr5:114548800-114575400	Weak transcription	Brain Substantia Nigra	brain
13	chr5:114549400-114597200	Weak transcription	Aorta	Aorta
14	chr5:114549600-114574400	Weak transcription	HMEC	breast
15	chr5:114550200-114575400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:114552200-114574600	Weak transcription	Fetal Stomach	stomach
17	chr5:114552200-114581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:114554200-114574600	Weak transcription	Right Ventricle	heart
19	chr5:114555800-114579800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:114556200-114578000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:114556400-114575600	Weak transcription	Fetal Brain Male	brain
22	chr5:114557000-114577400	Weak transcription	Fetal Heart	heart
23	chr5:114557800-114579400	Weak transcription	Gastric	stomach
24	chr5:114558000-114579400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:114559000-114587600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:114559400-114578200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:114559400-114579400	Weak transcription	Spleen	Spleen
28	chr5:114560600-114577400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:114561800-114574600	Weak transcription	Fetal Intestine Small	intestine
30	chr5:114562400-114577600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:114562400-114577600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr5:114563200-114578400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:114563400-114574600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:114563400-114574600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:114563400-114575400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:114563400-114578600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:114563400-114591600	Weak transcription	Brain Anterior Caudate	brain
38	chr5:114563400-114597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:114565000-114575000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:114565000-114575600	Weak transcription	HSMMtube	muscle
41	chr5:114565200-114597400	Weak transcription	Colonic Mucosa	Colon
42	chr5:114565600-114574600	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:114565600-114574600	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:114565800-114575400	Weak transcription	Fetal Brain Female	brain
45	chr5:114566000-114574000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:114566000-114574000	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:114566000-114574600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:114566000-114574600	Weak transcription	Ovary	ovary
49	chr5:114566000-114574600	Weak transcription	Thymus	Thymus
50	chr5:114566000-114576200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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