Variant report

Variant	rs524705
Chromosome Location	chr1:168665974-168665975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs512129	0.86[JPT][hapmap]
rs528953	0.86[JPT][hapmap]
rs530022	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs542149	0.81[JPT][hapmap]
rs545833	0.86[JPT][hapmap]
rs580360	0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs581753	0.81[JPT][hapmap]
rs586318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs598416	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs603259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs604627	0.81[ASN][1000 genomes]
rs606012	0.81[ASN][1000 genomes]
rs607484	0.86[JPT][hapmap]
rs612680	0.86[ASN][1000 genomes]
rs627098	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs630159	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap]
rs631451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656529	0.81[ASN][1000 genomes]
rs680531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681445	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682367	0.81[ASN][1000 genomes]
rs686226	0.81[JPT][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	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs524705	ALDH9A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168659400-168669400	Weak transcription	Small Intestine	intestine
2	chr1:168661800-168666200	Enhancers	Colon Smooth Muscle	Colon
3	chr1:168663000-168666200	Enhancers	Fetal Stomach	stomach
4	chr1:168663000-168666400	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:168663200-168669600	Weak transcription	Liver	Liver
6	chr1:168664000-168669400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:168664000-168669600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:168664600-168667600	Enhancers	Fetal Intestine Small	intestine
9	chr1:168664800-168666000	Enhancers	Fetal Intestine Large	intestine
10	chr1:168664800-168666200	Enhancers	Stomach Smooth Muscle	stomach
11	chr1:168665000-168666000	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr1:168665000-168666200	Enhancers	Fetal Lung	lung
13	chr1:168665200-168667000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:168665400-168666600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:168665400-168669800	Weak transcription	Adipose Nuclei	Adipose
16	chr1:168665400-168669800	Weak transcription	Stomach Mucosa	stomach
17	chr1:168665600-168666200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:168665600-168666200	Enhancers	Fetal Kidney	kidney
19	chr1:168665600-168667200	Weak transcription	Pancreas	Pancrea
20	chr1:168665600-168668600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:168665600-168673200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:168665600-168677600	Weak transcription	Fetal Heart	heart
23	chr1:168665800-168669600	Weak transcription	HepG2	liver

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