Variant report

Variant	rs9788091
Chromosome Location	chr12:21571978-21571979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:21571737-21572173	K562	blood:	n/a	n/a
2	YY1	chr12:21571974-21572594	K562	blood:	n/a	n/a
3	ARID3A	chr12:21571441-21572153	K562	blood:	n/a	n/a
4	POLR2A	chr12:21571953-21572259	K562	blood:	n/a	n/a
5	YY1	chr12:21571948-21572659	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBP	chr12:21571961-21572654	K562	blood:	n/a	n/a
7	YY1	chr12:21571951-21572328	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:21476298..21478074-chr12:21570042..21572071,2	K562	blood:
2	chr12:21569338..21572113-chr12:21589171..21592854,4	K562	blood:
3	chr12:21569338..21572113-chr12:21589171..21592483,4	K562	blood:

No data

Variant related genes	Relation type
SLCO1A2	TF binding region
ENSG00000084453	Chromatin interaction
ENSG00000121350	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10437776	0.81[CHD][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap]
rs10770808	0.83[JPT][hapmap]
rs10841808	0.83[JPT][hapmap]
rs10841809	0.83[JPT][hapmap]
rs10841810	0.83[JPT][hapmap]
rs7314170	0.83[CHD][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519603	chr12:21526472-21584709	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv898894	chr12:21545532-21583242	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9788091	PYROXD1	cis	lymphoblastoid	seeQTL
rs9788091	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs9788091	RECQL	cis	cerebellum	SCAN
rs9788091	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs9788091	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs9788091	PYROXD1	cis	cerebellum	SCAN
rs9788091	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs9788091	PYROXD1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21564800-21572200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:21570000-21572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:21570800-21572600	Active TSS	K562	blood
4	chr12:21571200-21572000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:21571600-21572600	Active TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links