Variant report

Variant	rs7031924
Chromosome Location	chr9:97403254-97403255
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	CTBP2	chr9:97402108-97403283	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
FBP1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10114605	0.84[EUR][1000 genomes]
rs10123016	0.93[EUR][1000 genomes]
rs10123666	0.91[EUR][1000 genomes]
rs10761345	0.84[EUR][1000 genomes]
rs10761347	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10761348	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs10993267	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs10993271	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993276	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1410972	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402381	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3739747	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3780554	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3780555	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4129220	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4744360	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744363	0.81[ASN][1000 genomes]
rs6479561	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7025121	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7041301	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7041595	0.83[AMR][1000 genomes];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	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7031924	XPA	cis	parietal	SCAN
rs7031924	CENPP	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97402200-97403400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:97402200-97410400	Weak transcription	Esophagus	oesophagus
3	chr9:97402400-97406600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr9:97402400-97420000	Weak transcription	Right Atrium	heart
5	chr9:97402600-97403400	Enhancers	Fetal Intestine Small	intestine
6	chr9:97402600-97403600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:97402600-97411000	Weak transcription	Gastric	stomach
8	chr9:97402600-97415400	Weak transcription	Spleen	Spleen
9	chr9:97402800-97403400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr9:97402800-97405600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:97402800-97411600	Weak transcription	Primary B cells from cord blood	blood
12	chr9:97403000-97403400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr9:97403000-97404800	Weak transcription	Lung	lung
14	chr9:97403000-97405000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:97403000-97406800	Weak transcription	Fetal Intestine Large	intestine
16	chr9:97403000-97406800	Weak transcription	Placenta	Placenta
17	chr9:97403000-97410600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:97403200-97403400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
19	chr9:97403200-97403600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr9:97403200-97405600	Weak transcription	Stomach Mucosa	stomach
21	chr9:97403200-97406600	Weak transcription	Duodenum Mucosa	Duodenum

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