Variant report

Variant	rs2328829
Chromosome Location	chr6:24724034-24724035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:24722796-24724039	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
2	chr6:24721787..24724500-chr6:24751636..24753786,2	MCF-7	breast:
3	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
4	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
5	chr6:24723437..24726062-chr6:24765366..24768785,3	K562	blood:

No data

Variant related genes	Relation type
C6orf62	TF binding region
ENSG00000272402	Chromatin interaction
ENSG00000272345	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000218806	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12190789	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12202375	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12203056	0.98[ASN][1000 genomes]
rs17491647	0.82[AMR][1000 genomes]
rs2294687	0.82[AMR][1000 genomes]
rs3813684	0.86[ASN][1000 genomes]
rs3813687	0.84[AMR][1000 genomes]
rs4466246	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6909127	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72830600	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72832608	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72832611	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72832613	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7774610	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2328829	C6orf62	cis	lung	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24722400-24724200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:24722400-24724800	Weak transcription	Right Atrium	heart
3	chr6:24722400-24726200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:24722400-24726600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:24722600-24725600	Weak transcription	GM12878-XiMat	blood
6	chr6:24722600-24727600	Weak transcription	Fetal Intestine Large	intestine
7	chr6:24722600-24727600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:24722600-24727800	Weak transcription	Stomach Mucosa	stomach
9	chr6:24722600-24728200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:24722800-24727800	Weak transcription	HepG2	liver

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