Variant report

Variant	rs12443848
Chromosome Location	chr16:80595177-80595178
allele	G/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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:80589493..80592966-chr16:80593921..80596964,3	MCF-7	breast:
2	chr16:80593040..80595743-chr16:80600736..80603732,2	K562	blood:
3	chr16:80576616..80579351-chr16:80593938..80597383,3	MCF-7	breast:
4	chr16:80594243..80596595-chr16:80599585..80602236,2	K562	blood:
5	chr16:80588433..80592032-chr16:80592068..80595320,4	K562	blood:
6	chr16:80593676..80596340-chr16:80598060..80599713,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDYL2-2	chr16:80595134-80595182	NONHSAT143893

No data

Variant related genes	Relation type
ENSG00000168589	Chromatin interaction
ENSG00000260737	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10871389	0.90[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10871390	0.95[CEU][hapmap];0.88[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11150295	0.81[ASW][hapmap];0.90[CEU][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11649558	0.85[CEU][hapmap]
rs11863816	0.89[EUR][1000 genomes]
rs11866588	0.89[EUR][1000 genomes]
rs11866734	0.80[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs11866994	0.90[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs12051207	0.87[EUR][1000 genomes]
rs12102506	0.86[EUR][1000 genomes]
rs12444563	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445674	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12448344	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12597089	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12597602	0.89[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12598311	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12600027	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934612	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13335321	0.91[ASN][1000 genomes]
rs28448585	0.90[EUR][1000 genomes]
rs28531767	0.84[EUR][1000 genomes]
rs28542735	0.98[EUR][1000 genomes]
rs28581872	0.83[EUR][1000 genomes]
rs28583998	0.91[EUR][1000 genomes]
rs28589320	0.98[EUR][1000 genomes]
rs28657821	0.89[EUR][1000 genomes]
rs28658033	0.83[EUR][1000 genomes]
rs28668848	0.84[EUR][1000 genomes]
rs28683132	0.86[EUR][1000 genomes]
rs28759267	0.89[EUR][1000 genomes]
rs4280255	0.95[CEU][hapmap]
rs4316772	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4352063	0.86[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4392092	0.82[JPT][hapmap]
rs4427819	0.90[CEU][hapmap];0.86[YRI][hapmap]
rs4458005	0.81[ASW][hapmap];0.90[CEU][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4517810	0.85[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs4533296	0.90[CEU][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4534859	0.93[ASW][hapmap];0.89[CHB][hapmap];0.81[GIH][hapmap];0.87[YRI][hapmap]
rs4541087	0.83[EUR][1000 genomes]
rs4567728	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4622526	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4889160	0.90[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs6564762	0.81[ASW][hapmap];0.90[CEU][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6564763	0.81[ASW][hapmap];0.90[CEU][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7187807	0.90[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs7190759	0.81[ASW][hapmap];0.90[CEU][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8045496	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs8182107	0.85[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs966670	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9931700	0.89[EUR][1000 genomes]
rs9932143	0.85[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs9933884	0.85[CEU][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs9935465	0.89[CHB][hapmap];0.87[YRI][hapmap]
rs9937217	0.88[EUR][1000 genomes]
rs9972743	0.86[EUR][1000 genomes]
rs9972747	0.87[EUR][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	nsv907001	chr16:80405292-80620611	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv833300	chr16:80475066-80601036	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12443848	C16orf61	cis	cerebellum	SCAN
rs12443848	TERF2IP	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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