Variant report

Variant	rs619146
Chromosome Location	chr5:112584120-112584121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10519347	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs2091803	0.89[YRI][hapmap]
rs498360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637634	0.87[CHB][hapmap]
rs665394	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7729163	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs619146	SNX17	trans	parietal	SCAN
rs619146	SP2	trans	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:112572400-112590400	Weak transcription	Liver	Liver
3	chr5:112572600-112585800	Weak transcription	Pancreas	Pancrea
4	chr5:112575400-112585400	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:112578600-112584200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:112578800-112584800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:112579600-112585400	Weak transcription	Esophagus	oesophagus
8	chr5:112579600-112587000	Weak transcription	Aorta	Aorta
9	chr5:112580600-112597400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:112581400-112584400	Enhancers	Left Ventricle	heart
11	chr5:112581400-112590800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:112581600-112585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:112582200-112585200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:112582200-112585400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:112582200-112586400	Weak transcription	HMEC	breast
16	chr5:112582400-112585000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:112582400-112585400	Weak transcription	Fetal Kidney	kidney
18	chr5:112582600-112585200	Weak transcription	HUVEC	blood vessel
19	chr5:112582600-112585600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:112582600-112585800	Weak transcription	Fetal Lung	lung
21	chr5:112582800-112584400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:112582800-112585200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:112582800-112585400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:112582800-112585400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:112582800-112585400	Weak transcription	Stomach Mucosa	stomach
26	chr5:112582800-112585600	Weak transcription	HSMM	muscle
27	chr5:112582800-112585800	Weak transcription	HSMMtube	muscle
28	chr5:112582800-112586000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:112582800-112586000	Weak transcription	Placenta	Placenta
30	chr5:112582800-112586400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:112582800-112586400	Weak transcription	NHEK	skin
32	chr5:112582800-112601000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:112583000-112584400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:112583000-112584400	Weak transcription	Osteobl	bone
35	chr5:112583000-112584800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:112583000-112585000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:112583000-112585200	Weak transcription	Fetal Stomach	stomach
38	chr5:112583000-112585400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:112583000-112585400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:112583000-112585400	Weak transcription	NHDF-Ad	bronchial
41	chr5:112583000-112585600	Weak transcription	Adipose Nuclei	Adipose
42	chr5:112583000-112586200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:112583000-112586400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:112583200-112585800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:112583200-112586400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr5:112583200-112587000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:112583600-112585200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:112583600-112585200	Weak transcription	Right Atrium	heart
50	chr5:112583600-112585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links