Variant report

Variant	rs12238579
Chromosome Location	chr9:100652058-100652059
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100649531..100652518-chr9:100653450..100655843,2	MCF-7	breast:
2	chr9:100651715..100653516-chr9:100817722..100819986,2	K562	blood:
3	chr9:100472975..100473600-chr9:100651604..100652809,3	MCF-7	breast:
4	chr9:100651977..100652889-chr9:100663107..100663913,3	MCF-7	breast:
5	chr9:100648546..100652838-chr9:100654754..100658082,3	K562	blood:
6	chr9:100464367..100467056-chr9:100650913..100653289,2	K562	blood:
7	chr9:100645728..100648046-chr9:100651565..100653285,2	K562	blood:
8	chr9:100648000..100649701-chr9:100650318..100652394,2	MCF-7	breast:
9	chr9:100637402..100640995-chr9:100649849..100652626,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10113907	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10119795	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10818239	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10984193	0.82[YRI][hapmap]
rs11999801	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12003789	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300874	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13301569	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1443434	0.81[CHB][hapmap]
rs1443435	0.81[CHB][hapmap]
rs1561958	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1561959	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2120263	0.88[CHB][hapmap]
rs2282192	0.88[CHB][hapmap]
rs2417577	0.81[CHB][hapmap]
rs3183927	0.81[CHB][hapmap]
rs3758249	0.81[CHB][hapmap]
rs3758251	0.81[CHB][hapmap]
rs3758253	0.81[CHB][hapmap]
rs3758254	0.81[CHB][hapmap]
rs3780420	0.81[CHB][hapmap]
rs4631576	0.81[CHB][hapmap]
rs4743140	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4743147	0.84[CHB][hapmap]
rs6478450	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67449879	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7020644	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7033315	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7357707	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7853349	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7870125	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs874004	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs894673	0.81[CHB][hapmap]
rs907577	0.81[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12238579	C9orf156	cis	Frontal Cortex	GTEx
rs12238579	C9orf156	cis	Skin Sun Exposed Lower leg	GTEx
rs12238579	C9orf156	cis	Brain Pons	GTEx
rs12238579	Hs.43687	cis	multi-tissue	Pritchard
rs12238579	C9orf156	cis	Thyroid	GTEx
rs12238579	FOXE1	cis	Esophagus Mucosa	GTEx
rs12238579	C9orf156	cis	Esophagus Muscularis	GTEx
rs12238579	C9orf156	cis	Cerebellum	GTEx
rs12238579	C9orf156	cis	Temporal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100637600-100658000	Weak transcription	Gastric	stomach
2	chr9:100637800-100652800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:100650400-100652200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:100651800-100652800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:100651800-100653000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:100651800-100653000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr9:100652000-100653000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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