Variant report

Variant	rs11102724
Chromosome Location	chr1:114596480-114596481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114583212..114585104-chr1:114595811..114597428,2	MCF-7	breast:
2	chr1:114587184..114588685-chr1:114594720..114597075,2	MCF-7	breast:
3	chr1:114594128..114597061-chr1:114598670..114602014,3	K562	blood:
4	chr1:114596275..114599885-chr1:114602118..114604793,4	MCF-7	breast:
5	chr1:114595324..114597061-chr1:114598670..114600429,2	K562	blood:
6	chr1:114594344..114596530-chr1:114631234..114632774,2	MCF-7	breast:
7	chr1:114574403..114579108-chr1:114596233..114599527,4	MCF-7	breast:
8	chr1:114595497..114597013-chr1:114615849..114618370,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10858029	0.87[EUR][1000 genomes]
rs11102720	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12066263	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12239127	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12749841	0.90[ASN][1000 genomes]
rs1503835	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4839352	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4839354	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4839355	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4839358	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4839359	0.82[EUR][1000 genomes]
rs61819248	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521423	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2754686	chr1:114531958-114602958	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv463284	chr1:114585590-114623867	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv547568	chr1:114585590-114623867	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv547569	chr1:114587766-114625425	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11102724	CSDE1	cis	cerebellum	SCAN
rs11102724	C1orf103	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114591000-114597600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:114592400-114596800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:114592400-114603600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:114596400-114596600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:114596400-114596600	Enhancers	Liver	Liver
6	chr1:114596400-114596600	Enhancers	Ovary	ovary

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links