Variant report

Variant	rs9689461
Chromosome Location	chr6:4774565-4774566
allele	C/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	CHD1	chr6:4773958-4774656	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr6:4772779-4776923	H1-hESC	embryonic stem cell:	n/a	chr6:4775707-4775717 chr6:4775835-4775846

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4475486..4477630-chr6:4774016..4775629,2	MCF-7	breast:

Variant related genes	Relation type
CDYL	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1999867	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1999868	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs395180	0.88[ASN][1000 genomes]
rs4502986	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57992430	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58544878	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59797348	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60731840	0.88[EUR][1000 genomes]
rs62384842	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62384843	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62384848	0.83[EUR][1000 genomes]
rs62384849	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62384850	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62384853	0.88[EUR][1000 genomes]
rs6907313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908435	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921417	0.86[EUR][1000 genomes]
rs6927577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747102	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7750308	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9502235	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9502236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502237	0.94[EUR][1000 genomes]
rs9504235	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9504238	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9504244	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9504245	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9504247	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9504248	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9689911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017938	chr6:4729592-4774914	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4769800-4775000	Weak transcription	Aorta	Aorta
2	chr6:4772600-4776200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:4772800-4777200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:4772800-4777800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:4773000-4774600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:4773000-4777400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:4773000-4777600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:4773200-4775000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:4773200-4777400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:4773200-4777400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:4773200-4777400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:4773200-4777600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:4773200-4778200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:4774000-4775000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:4774000-4775600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:4774200-4774600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:4774200-4774800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:4774200-4775000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:4774200-4778000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links