Variant report

Variant	rs9388989
Chromosome Location	chr6:132697582-132697583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2275394	1.00[ASW][hapmap];0.89[JPT][hapmap]
rs3734744	0.83[CEU][hapmap]
rs6569792	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs6937164	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375877	0.94[MEX][hapmap]
rs9493297	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830811	chr6:132623160-132787539	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv886675	chr6:132683762-132730947	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv604668	chr6:132687248-132731358	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv818455	chr6:132694751-132702249	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	esv3387784	chr6:132696959-132698957	Weak transcription Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	esv5479	chr6:132697375-132698222	Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
7	esv2257358	chr6:132697456-132698138	Weak transcription	n/a	n/a	inside rSNPs	diseases
8	esv3473375	chr6:132697515-132698041	Weak transcription	n/a	n/a	inside rSNPs	diseases
9	esv3517192	chr6:132697534-132698038	Weak transcription	n/a	n/a	inside rSNPs	diseases
10	esv3517193	chr6:132697537-132698062	Weak transcription	n/a	n/a	inside rSNPs	diseases
11	esv3473373	chr6:132697553-132698037	Weak transcription	n/a	n/a	inside rSNPs	diseases
12	esv3517194	chr6:132697560-132697986	Weak transcription	n/a	n/a	inside rSNPs	diseases
13	esv3473371	chr6:132697565-132698023	Weak transcription	n/a	n/a	inside rSNPs	diseases
14	esv3517197	chr6:132697572-132698003	Weak transcription	n/a	n/a	inside rSNPs	diseases
15	esv3473376	chr6:132697581-132697979	Weak transcription	n/a	n/a	inside rSNPs	diseases
16	esv2791	chr6:132697583-132698146	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9388989	CTGF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132677400-132701200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:132682200-132705800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:132692000-132701200	Weak transcription	Osteobl	bone
4	chr6:132692200-132698400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:132692600-132709200	Weak transcription	Fetal Kidney	kidney
6	chr6:132693200-132709400	Weak transcription	Fetal Lung	lung
7	chr6:132694200-132699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:132694400-132705400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:132694600-132705800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:132694800-132699200	Weak transcription	NHDF-Ad	bronchial

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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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