Variant report

Variant	rs7533274
Chromosome Location	chr1:62673225-62673226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF7	chr1:62672886-62673249	H1-hESC	embryonic stem cell:	n/a	n/a
2	TRIM28	chr1:62672769-62673262	K562	blood:	n/a	n/a
3	CBX3	chr1:62672865-62673242	K562	blood:	n/a	n/a
4	POLR2A	chr1:62671110-62680443	H1-hESC	embryonic stem cell:	n/a	n/a
5	KAP1	chr1:62672651-62673275	HEK293	kidney:	n/a	n/a
6	POLR2A	chr1:62672293-62675216	H1-hESC	embryonic stem cell:	n/a	n/a
7	ATF2	chr1:62672636-62673515	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:62672294-62680406	H1-hESC	embryonic stem cell:	n/a	n/a
9	SETDB1	chr1:62672739-62673276	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000200174	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11207933	0.86[CHB][hapmap]
rs13374682	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2457826	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2457827	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4915604	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7542665	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv870842	chr1:62644118-62679202	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7533274	OMA1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62661000-62675600	Weak transcription	Right Atrium	heart
2	chr1:62664800-62677800	Weak transcription	Placenta	Placenta
3	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:62667000-62674200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:62667400-62676200	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr1:62668400-62677200	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr1:62669000-62674600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:62669000-62675600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:62669400-62673800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:62670400-62677200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:62670600-62673400	Strong transcription	Fetal Lung	lung
12	chr1:62670600-62674400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:62670600-62675400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:62670600-62676200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:62671600-62675400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:62671800-62673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:62671800-62673400	Weak transcription	Fetal Stomach	stomach
18	chr1:62671800-62673800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:62671800-62673800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:62671800-62678200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr1:62672200-62675600	Weak transcription	Fetal Kidney	kidney
22	chr1:62672200-62677400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr1:62672800-62673800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:62672800-62674400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr1:62672800-62674800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:62672800-62675000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:62673200-62674400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:62673200-62675400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:62673200-62676400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links