Variant report

Variant	rs6542919
Chromosome Location	chr2:100820201-100820202
allele	A/G
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	EP300	chr2:100819968-100821410	SK-N-SH	brain:	n/a	chr2:100821376-100821390 chr2:100820693-100820707

Variant related genes	Relation type
LINC01104	TF binding region

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10170878	1.00[JPT][hapmap]
rs10173499	1.00[JPT][hapmap]
rs10865039	1.00[JPT][hapmap]
rs12463633	1.00[JPT][hapmap]
rs12472141	1.00[JPT][hapmap]
rs13397337	1.00[JPT][hapmap]
rs2309817	1.00[JPT][hapmap]
rs2309822	1.00[JPT][hapmap]
rs2309823	1.00[JPT][hapmap]
rs2309824	1.00[JPT][hapmap]
rs4851287	1.00[JPT][hapmap]
rs6542918	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542923	1.00[JPT][hapmap]
rs6542924	1.00[JPT][hapmap]
rs6724490	1.00[JPT][hapmap]
rs6727712	1.00[JPT][hapmap]
rs7559464	1.00[JPT][hapmap]
rs7562372	1.00[JPT][hapmap]
rs7582180	1.00[JPT][hapmap]
rs7588623	1.00[JPT][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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100815000-100823600	Weak transcription	Fetal Heart	heart
2	chr2:100815200-100820400	Weak transcription	Fetal Brain Female	brain
3	chr2:100815600-100823800	Weak transcription	Left Ventricle	heart
4	chr2:100818600-100825000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:100819800-100821600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:100820200-100825400	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links