Variant report

Variant	rs6601604
Chromosome Location	chr8:11575518-11575519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11569396..11573726-chr8:11575318..11577927,4	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12550668	0.84[MEX][hapmap]
rs13267318	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13270069	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2409807	0.90[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.95[ASN][1000 genomes]
rs4410868	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6983129	0.81[CHB][hapmap];0.80[GIH][hapmap]

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	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1017865	chr8:11377795-11579954	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6601604	FLJ10661	cis	cerebellum	SCAN
rs6601604	DEFB136	cis	parietal	SCAN
rs6601604	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11568000-11577600	Weak transcription	Gastric	stomach
2	chr8:11572200-11576600	Enhancers	Fetal Intestine Small	intestine
3	chr8:11572400-11577400	Weak transcription	Placenta	Placenta
4	chr8:11573200-11576000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:11574000-11575600	Enhancers	Right Ventricle	heart
6	chr8:11574000-11575800	Bivalent Enhancer	Fetal Intestine Large	intestine
7	chr8:11574000-11576000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
8	chr8:11574000-11577800	Enhancers	Stomach Mucosa	stomach
9	chr8:11574000-11578000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:11574000-11578400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr8:11574400-11576800	Flanking Active TSS	HepG2	liver
12	chr8:11574600-11576800	Enhancers	Ovary	ovary
13	chr8:11575000-11575600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
14	chr8:11575000-11576200	Flanking Active TSS	Liver	Liver
15	chr8:11575200-11575800	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr8:11575200-11576000	Enhancers	Right Atrium	heart
17	chr8:11575200-11576200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
18	chr8:11575200-11576800	Enhancers	Left Ventricle	heart
19	chr8:11575200-11581800	Enhancers	Fetal Heart	heart
20	chr8:11575400-11575600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
21	chr8:11575400-11575600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
22	chr8:11575400-11575600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr8:11575400-11575600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr8:11575400-11577400	Weak transcription	Pancreas	Pancrea

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