Variant report

Variant	rs12542146
Chromosome Location	chr8:10447763-10447764
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10447712..10448262-chr8:10591419..10591945,2	MCF-7	breast:
2	chr8:10445268..10448079-chr8:10682577..10684280,3	K562	blood:
3	chr8:10447717..10449945-chr8:10695392..10697388,2	MCF-7	breast:
4	chr8:10447388..10448227-chr8:10671479..10672292,5	MCF-7	breast:
5	chr8:10447015..10448532-chr8:10696136..10697603,15	K562	blood:
6	chr8:10447720..10448261-chr8:10675847..10676686,2	K562	blood:
7	chr8:10447282..10448390-chr8:10682147..10683493,10	MCF-7	breast:
8	chr8:10447312..10448291-chr8:10671241..10672318,3	MCF-7	breast:
9	chr8:10447691..10448293-chr8:10586014..10586821,3	MCF-7	breast:
10	chr8:10446054..10448904-chr8:10503289..10505926,2	K562	blood:
11	chr8:10447366..10448118-chr8:10670992..10671978,2	K562	blood:
12	chr8:10447404..10448576-chr8:10655982..10656998,11	MCF-7	breast:
13	chr8:10447281..10448089-chr8:10696064..10697196,3	MCF-7	breast:
14	chr8:10447726..10448226-chr8:10680360..10680981,2	K562	blood:
15	chr8:10447286..10448405-chr8:10682073..10684028,19	K562	blood:

No data

No data

No data

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11250045	0.89[ASN][1000 genomes]
rs11776032	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11780019	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11995259	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35626194	0.83[AMR][1000 genomes]
rs4841389	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55855130	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57550128	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62490812	0.82[ASN][1000 genomes]
rs62490814	0.81[ASN][1000 genomes]
rs9644729	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9650655	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv610268	chr8:10331636-10486652	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1025251	chr8:10343591-10488557	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv610269	chr8:10416017-10461484	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv610271	chr8:10438796-10459203	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv890351	chr8:10439902-10482372	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12542146	C8orf12	cis	cerebellum	SCAN
rs12542146	FAM167A	cis	parietal	SCAN
rs12542146	PRSS55	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10439000-10453000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:10445200-10447800	Weak transcription	Adipose Nuclei	Adipose
3	chr8:10445200-10450400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr8:10445400-10447800	Weak transcription	Liver	Liver
5	chr8:10445600-10447800	Weak transcription	HUVEC	blood vessel
6	chr8:10446800-10448200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:10447400-10447800	Enhancers	Fetal Muscle Leg	muscle
8	chr8:10447400-10448000	Enhancers	Pancreas	Pancrea
9	chr8:10447400-10449200	Enhancers	Lung	lung
10	chr8:10447600-10448000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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