Variant report

Variant	rs13374935
Chromosome Location	chr1:45733403-45733404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45716599..45723837-chr1:45726714..45733883,8	K562	blood:
2	chr1:45732068..45734921-chr1:45735419..45738546,3	K562	blood:
3	chr1:45476441..45479268-chr1:45730943..45735268,3	K562	blood:
4	chr1:45731206..45733732-chr1:45740746..45742362,2	K562	blood:

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1144868	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs11802089	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11806438	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11810239	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1226670	0.81[EUR][1000 genomes]
rs1226733	0.83[EUR][1000 genomes]
rs1226734	0.83[EUR][1000 genomes]
rs1226746	0.84[EUR][1000 genomes]
rs1226747	0.93[CEU][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs1226748	0.84[EUR][1000 genomes]
rs1612575	0.87[CHD][hapmap]
rs1782459	0.81[EUR][1000 genomes]
rs1938296	0.88[ASN][1000 genomes]
rs1938301	0.91[JPT][hapmap]
rs1938303	0.91[EUR][1000 genomes]
rs1938407	0.93[ASN][1000 genomes]
rs2105458	0.91[JPT][hapmap]
rs2186219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2356302	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs238249	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs2997458	0.90[ASN][1000 genomes]
rs2997461	0.91[JPT][hapmap]
rs2997465	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs3009969	0.91[JPT][hapmap]
rs3009974	0.90[JPT][hapmap]
rs3009979	0.91[JPT][hapmap]
rs3121732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3121736	0.82[ASN][1000 genomes]
rs3121769	0.90[ASN][1000 genomes]
rs3128438	0.82[ASN][1000 genomes]
rs3128439	0.88[ASN][1000 genomes]
rs3128440	0.88[ASN][1000 genomes]
rs34134455	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs346684	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs346693	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs346695	0.81[EUR][1000 genomes]
rs346696	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs346697	0.80[EUR][1000 genomes]
rs346698	0.80[EUR][1000 genomes]
rs346702	0.93[CEU][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs346703	0.87[CHD][hapmap]
rs346706	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs346707	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs346712	0.81[EUR][1000 genomes]
rs346716	0.81[EUR][1000 genomes]
rs346717	0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs346719	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs346721	0.81[EUR][1000 genomes]
rs346724	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs346725	0.87[CHD][hapmap]
rs346732	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs346733	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs346734	0.81[EUR][1000 genomes]
rs346736	0.91[JPT][hapmap]
rs365108	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs3850856	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs4233496	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs4233497	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs4376776	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4376777	0.81[ASN][1000 genomes]
rs454624	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4603171	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660295	0.88[EUR][1000 genomes]
rs4660839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4660841	0.90[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4660842	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs55932948	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56086213	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56363452	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56791336	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57754814	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58374842	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58579477	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58934647	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60115828	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61003126	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61789780	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61789781	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61789815	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61789823	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61789838	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61789841	0.85[EUR][1000 genomes]
rs6429561	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6429562	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs6429563	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs72684493	0.88[EUR][1000 genomes]
rs72686440	0.85[EUR][1000 genomes]
rs974143	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
4	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13374935	NSUN4	cis	cerebellum	SCAN
rs13374935	TIE1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45731000-45733600	Enhancers	HUVEC	blood vessel
2	chr1:45731600-45733600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:45731800-45734200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:45732200-45733600	Enhancers	Osteobl	bone
5	chr1:45732400-45733600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:45732400-45734200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:45732400-45734200	Enhancers	Hela-S3	cervix
8	chr1:45732400-45739400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:45732400-45740600	Weak transcription	Stomach Mucosa	stomach
10	chr1:45732400-45748000	Weak transcription	Right Atrium	heart
11	chr1:45732600-45734200	Enhancers	K562	blood
12	chr1:45732800-45733800	Weak transcription	NH-A	brain
13	chr1:45732800-45734000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:45733000-45733600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:45733200-45733600	Enhancers	NHLF	lung
16	chr1:45733200-45734400	Enhancers	Ovary	ovary
17	chr1:45733200-45735400	Weak transcription	HepG2	liver
18	chr1:45733400-45733600	Enhancers	Small Intestine	intestine
19	chr1:45733400-45740800	Weak transcription	Fetal Intestine Small	intestine

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