Variant report

Variant	rs7030388
Chromosome Location	chr9:102667724-102667725
allele	A/T
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	CEBPB	chr9:102667677-102667922	HepG2	liver:	n/a	n/a
2	CEBPB	chr9:102667704-102667942	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:102580574..102584384-chr9:102666062..102670667,9	K562	blood:
2	chr9:102580667..102584355-chr9:102667685..102671328,3	K562	blood:
3	chr9:102665635..102667758-chr9:102670222..102671965,2	K562	blood:
4	chr9:102580482..102589062-chr9:102666380..102672134,16	MCF-7	breast:

Variant related genes	Relation type
STX17	TF binding region
ENSG00000119508	Chromatin interaction
ENSG00000237461	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10117638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117828	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs10120103	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10121601	0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10121880	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10122128	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123261	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10124366	0.81[ASN][1000 genomes]
rs10125981	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217337	0.94[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs10217366	0.93[ASN][1000 genomes]
rs10217692	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10512268	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1055187	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739791	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739793	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760698	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760700	0.94[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760704	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs10760705	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760706	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10819705	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819706	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819707	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819711	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988919	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988920	0.92[ASN][1000 genomes]
rs12352899	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830454	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1852863	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs1881751	0.90[ASN][1000 genomes]
rs1962051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997367	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1997368	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2031035	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs2416935	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416936	0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2416937	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416938	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416940	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416941	0.93[ASN][1000 genomes]
rs2416942	0.93[ASN][1000 genomes]
rs2900224	0.92[ASN][1000 genomes]
rs3739794	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3983846	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282626	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4452862	0.93[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs4585797	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742777	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742778	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743370	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6478987	0.93[ASN][1000 genomes]
rs6478988	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478990	0.93[ASN][1000 genomes]
rs7022208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022999	0.93[ASN][1000 genomes]
rs7027619	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs7027813	0.95[ASN][1000 genomes]
rs7038506	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7039716	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs7853264	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299335	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription 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	32 gene(s)	inside rSNPs	diseases
4	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	esv3366813	chr9:102657446-102670065	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7030388	STX17	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102648800-102667800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:102657400-102668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:102661000-102668200	Weak transcription	Aorta	Aorta
4	chr9:102666600-102668400	Weak transcription	Fetal Intestine Large	intestine
5	chr9:102667000-102668000	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links