Variant report

Variant	rs10788807
Chromosome Location	chr1:151477312-151477313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151430186..151432717-chr1:151476537..151479729,3	K562	blood:
2	1:151411623-151426875..1:151476039-151478607	GM12878	blood:

Variant related genes	Relation type
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1009289	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10127622	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10788808	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888418	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888419	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204827	1.00[JPT][hapmap]
rs11204828	1.00[JPT][hapmap]
rs11204834	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204835	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204837	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204838	0.87[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11204839	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11583133	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11801161	0.84[JPT][hapmap]
rs12026585	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032983	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037100	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118440	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128578	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730114	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1547832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573129	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1573130	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2211435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298167	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2298168	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2337359	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2878950	0.84[JPT][hapmap]
rs4970955	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs61261719	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6675984	0.83[ASN][1000 genomes]
rs7548090	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552458	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10788807	SV2A	cis	parietal	SCAN
rs10788807	TUFT1	cis	cerebellum	SCAN
rs10788807	SPRR2B	cis	parietal	SCAN
rs10788807	S100A2	cis	parietal	SCAN
rs10788807	OTUD7B	cis	cerebellum	SCAN
rs10788807	SCNM1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151468400-151482400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:151468600-151482400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:151470200-151482400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:151475400-151481600	Weak transcription	Stomach Mucosa	stomach
5	chr1:151475400-151481800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:151475400-151483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:151475800-151477400	Enhancers	NHEK	skin
8	chr1:151475800-151482000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:151475800-151482800	Weak transcription	Hela-S3	cervix
10	chr1:151475800-151483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:151476000-151481800	Weak transcription	Colonic Mucosa	Colon
12	chr1:151476200-151477400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:151476600-151477400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:151476600-151477600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:151476600-151481400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:151476800-151477600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:151476800-151477600	Enhancers	K562	blood
18	chr1:151477000-151477400	Enhancers	A549	lung
19	chr1:151477000-151481400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:151477200-151477400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:151477200-151477400	Enhancers	Small Intestine	intestine
22	chr1:151477200-151482600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:151477200-151483200	Weak transcription	HMEC	breast

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