Variant report

Variant	rs9359727
Chromosome Location	chr6:87780737-87780738
allele	G/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	MYC	chr6:87780555-87780745	K562	blood:	n/a	n/a
2	TBP	chr6:87780539-87780823	K562	blood:	n/a	n/a
3	MAZ	chr6:87780590-87780752	K562	blood:	n/a	n/a
4	JUND	chr6:87780503-87780811	K562	blood:	n/a	n/a
5	EP300	chr6:87780491-87780878	K562	blood:	n/a	n/a
6	RCOR1	chr6:87780666-87780741	K562	blood:	n/a	n/a
7	ATF1	chr6:87780545-87780793	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000217776	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11753367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11968873	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13199707	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13218179	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35974519	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4986869	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6631	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6902324	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73497586	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9294364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9294365	1.00[CEU][hapmap];0.86[CHD][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932742	0.91[GIH][hapmap]
rs9342103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9344670	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9344671	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9351112	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9353447	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9359728	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9359730	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9362385	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9362386	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444466	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444467	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444468	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450611	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450612	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9359727	C6orf162	cis	parietal	SCAN
rs9359727	C6orf162	cis	cerebellum	SCAN
rs9359727	MDN1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87769000-87784000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:87779800-87781600	Enhancers	Duodenum Mucosa	Duodenum
3	chr6:87779800-87781600	Enhancers	Fetal Intestine Large	intestine
4	chr6:87779800-87785200	Enhancers	Fetal Intestine Small	intestine
5	chr6:87780200-87781000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:87780400-87784000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:87780600-87780800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:87780600-87780800	Enhancers	Hela-S3	cervix
9	chr6:87780600-87783600	Weak transcription	Stomach Mucosa	stomach
10	chr6:87780600-87784000	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links