Variant report

Variant	rs9296232
Chromosome Location	chr6:37767054-37767055
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37760526..37762581-chr6:37765798..37767816,2	MCF-7	breast:
2	chr6:37765846..37768187-chr6:37771368..37772947,2	K562	blood:
3	chr6:37764796..37769141-chr6:37786360..37788768,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225945	Chromatin interaction
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10456096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10485029	0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs10807188	0.98[EUR][1000 genomes]
rs1187421	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs1187422	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1187423	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12192182	0.89[EUR][1000 genomes]
rs12198907	0.86[EUR][1000 genomes]
rs12200258	0.96[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs12206818	0.88[EUR][1000 genomes]
rs12211248	0.88[CHB][hapmap];0.89[EUR][1000 genomes]
rs12211981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12213835	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13210701	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[EUR][1000 genomes]
rs171831	0.84[EUR][1000 genomes]
rs1812599	0.88[EUR][1000 genomes]
rs2055206	0.84[CEU][hapmap]
rs2395686	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259673	0.85[EUR][1000 genomes]
rs259684	0.82[EUR][1000 genomes]
rs259686	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs259689	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs259690	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs259691	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs259695	0.84[EUR][1000 genomes]
rs259713	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs259715	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs259716	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2645107	0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs2645116	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs2842517	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs34871463	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458027	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458028	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6941057	0.81[CEU][hapmap]
rs7755089	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647619	0.87[EUR][1000 genomes]
rs966705	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9296232	TAF11	cis	cerebellum	SCAN
rs9296232	SLC26A8	cis	cerebellum	SCAN
rs9296232	KCNK17	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37759200-37768400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:37759600-37767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:37759600-37767200	Weak transcription	Right Atrium	heart
4	chr6:37759800-37768600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:37766000-37767400	Flanking Active TSS	HepG2	liver
6	chr6:37766400-37767200	Flanking Active TSS	Liver	Liver
7	chr6:37766400-37768200	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr6:37766400-37768800	Enhancers	Fetal Stomach	stomach
9	chr6:37766400-37775400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:37766600-37767400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:37766600-37767400	Enhancers	HSMMtube	muscle
12	chr6:37766800-37767800	Enhancers	Fetal Intestine Small	intestine
13	chr6:37767000-37767600	Enhancers	Stomach Mucosa	stomach
14	chr6:37767000-37767800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:37767000-37767800	Enhancers	Fetal Intestine Large	intestine

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