Variant report

Variant	rs9326879
Chromosome Location	chr5:112446323-112446324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10040400	0.86[EUR][1000 genomes]
rs10074318	0.84[JPT][hapmap]
rs10478110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10519334	0.84[JPT][hapmap]
rs11241191	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241192	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11743369	0.81[ASN][1000 genomes]
rs11953203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11960706	0.83[CEU][hapmap]
rs12109548	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12187718	0.85[EUR][1000 genomes]
rs12187866	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs12188482	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12517185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12517187	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13156718	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs13174483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13179421	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13183472	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13183638	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13184187	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36041392	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3884576	0.85[ASN][1000 genomes]
rs3922563	0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3922583	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4078253	0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4078254	0.80[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4235793	0.80[ASN][1000 genomes]
rs4262097	0.81[ASN][1000 genomes]
rs4705542	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4705543	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4705544	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4705545	0.80[ASN][1000 genomes]
rs4705778	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4705779	0.85[EUR][1000 genomes]
rs4705780	0.83[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs4705782	0.80[CEU][hapmap]
rs4705783	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs4705787	0.80[ASN][1000 genomes]
rs4705788	0.80[ASN][1000 genomes]
rs62374710	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6594682	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594683	0.80[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6860460	0.96[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs6869399	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6883605	0.80[CEU][hapmap]
rs7700271	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7704382	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7707142	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7731180	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9326877	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9326878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9885385	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9326879	SRP19	cis	parietal	SCAN
rs9326879	MXD3	trans	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
6	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
8	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
9	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
12	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
13	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
16	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
17	chr5:112438200-112450000	Weak transcription	Adipose Nuclei	Adipose
18	chr5:112438200-112450200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
20	chr5:112439600-112454600	Weak transcription	Esophagus	oesophagus
21	chr5:112439800-112452600	Weak transcription	Fetal Lung	lung
22	chr5:112440000-112450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:112440200-112446600	Weak transcription	Right Ventricle	heart
24	chr5:112440200-112447800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:112440200-112447800	Weak transcription	Right Atrium	heart
26	chr5:112440200-112448000	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:112440200-112450000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:112440200-112450000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:112440200-112450000	Weak transcription	Fetal Stomach	stomach
30	chr5:112440200-112454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:112441600-112447600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:112442400-112446600	Enhancers	Liver	Liver
33	chr5:112442800-112452600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:112443400-112448600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:112443600-112446400	Weak transcription	Left Ventricle	heart
36	chr5:112444400-112446400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr5:112444400-112446800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:112444400-112448600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:112444800-112448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:112444800-112450000	Weak transcription	Lung	lung
41	chr5:112445000-112448600	Weak transcription	HMEC	breast
42	chr5:112445600-112446600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:112445800-112447000	Enhancers	Fetal Heart	heart
44	chr5:112445800-112447200	Enhancers	Ovary	ovary
45	chr5:112446000-112446400	Enhancers	NHEK	skin
46	chr5:112446200-112448000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links