Variant report

Variant	rs9490225
Chromosome Location	chr6:121703855-121703856
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	GATA2	chr6:121703752-121704284	SH-SY5Y	brain:	n/a	n/a
2	KAP1	chr6:121703604-121704103	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000207403	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12527395	0.82[ASN][1000 genomes]
rs1555772	0.84[ASN][1000 genomes]
rs1925220	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1925221	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147709	0.85[ASN][1000 genomes]
rs4376375	0.81[AFR][1000 genomes]
rs56140776	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56785883	0.99[ASN][1000 genomes]
rs58735295	0.99[ASN][1000 genomes]
rs61047908	0.99[ASN][1000 genomes]
rs66584012	0.81[EUR][1000 genomes]
rs67199580	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67502032	0.81[EUR][1000 genomes]
rs67612546	0.87[ASN][1000 genomes]
rs68043442	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68096413	0.81[EUR][1000 genomes]
rs68165630	0.81[ASN][1000 genomes]
rs68192738	0.87[ASN][1000 genomes]
rs73530206	0.99[ASN][1000 genomes]
rs9482153	0.81[EUR][1000 genomes]
rs9482154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482155	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482156	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9482157	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9490219	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9490220	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9490221	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9490222	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9490226	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9490228	0.97[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	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv830789	chr6:121581450-121732320	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv969324	chr6:121703134-121711366	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9490225	TRDN	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121698800-121705400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:121702600-121706000	Enhancers	Fetal Intestine Large	intestine
3	chr6:121702600-121706000	Enhancers	Fetal Intestine Small	intestine
4	chr6:121703000-121705600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:121703800-121704200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr6:121703800-121704800	Weak transcription	A549	lung
7	chr6:121703800-121705600	Enhancers	Rectal Mucosa Donor 29	rectum

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