Variant report

Variant	rs61823898
Chromosome Location	chr1:222152268-222152269
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	NANOG	chr1:222152004-222152293	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr1:222152004-222152322	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr1:222152069-222152329	H1-hESC	embryonic stem cell:	n/a	n/a
4	POU5F1	chr1:222152217-222152609	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221914898..221917139-chr1:222150225..222152993,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238042	TF binding region
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10863674	0.91[EUR][1000 genomes]
rs11118911	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118921	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118922	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118923	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118924	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118925	0.94[EUR][1000 genomes]
rs11118929	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12070612	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12082069	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12083686	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12090915	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403104	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17441981	0.95[EUR][1000 genomes]
rs17442148	0.83[ASN][1000 genomes]
rs17495034	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2225999	0.91[EUR][1000 genomes]
rs34601597	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34736719	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4291507	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4565720	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59826275	0.86[ASN][1000 genomes]
rs7517045	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7538348	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222146200-222163800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:222147800-222152400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:222148800-222154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:222150600-222152400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:222150800-222152600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:222151200-222152400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:222151400-222152400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:222151400-222152400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:222152000-222152400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:222152200-222152400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:222152200-222152600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:222152200-222152800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links