Variant report

Variant	rs7565580
Chromosome Location	chr2:11625004-11625005
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11621665..11625691-chr2:11759993..11762950,4	MCF-7	breast:
2	chr1:40041963..40043870-chr2:11623878..11625841,2	MCF-7	breast:
3	chr2:11623545..11625174-chr5:160606467..160607967,2	MCF-7	breast:
4	chr2:11268656..11272146-chr2:11621524..11625212,4	MCF-7	breast:
5	chr16:72323629..72325628-chr2:11623411..11625010,2	MCF-7	breast:
6	chr2:11267451..11270365-chr2:11623207..11626147,3	MCF-7	breast:
7	chr2:11622883..11625359-chr2:11804160..11807192,3	MCF-7	breast:
8	chr11:77899272..77902143-chr2:11623062..11626037,2	MCF-7	breast:
9	chr2:11624474..11626052-chr2:11639612..11642018,2	K562	blood:
10	chr2:11624861..11626975-chr2:11632564..11634549,2	K562	blood:
11	chr2:11619432..11626810-chr2:11815160..11825829,15	MCF-7	breast:
12	chr2:11622770..11625345-chr2:11826653..11829595,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000134324	Chromatin interaction
ENSG00000230044	Chromatin interaction
ENSG00000090621	Chromatin interaction
ENSG00000228496	Chromatin interaction
ENSG00000118369	Chromatin interaction
ENSG00000188997	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10195636	0.82[EUR][1000 genomes]
rs1109098	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11675074	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11893713	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11903099	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3893103	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669730	0.82[EUR][1000 genomes]
rs4669731	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61138273	0.82[EUR][1000 genomes]
rs7587139	0.82[ASN][1000 genomes]
rs7590419	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7601812	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875624	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11623800-11636000	Weak transcription	Pancreas	Pancrea
2	chr2:11624000-11632200	Weak transcription	Right Ventricle	heart
3	chr2:11624000-11638600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:11624400-11625200	Bivalent Enhancer	Small Intestine	intestine
5	chr2:11624400-11631600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:11624600-11625200	Flanking Active TSS	Ovary	ovary
7	chr2:11624600-11625800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:11624600-11625800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:11624600-11626000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:11624600-11629600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:11624600-11630200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:11624800-11625400	Enhancers	Placenta	Placenta
13	chr2:11624800-11625800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:11625000-11625200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:11625000-11625200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:11625000-11625600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:11625000-11625600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:11625000-11625600	Enhancers	HepG2	liver

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

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