Variant report

Variant	rs16856946
Chromosome Location	chr3:110210285-110210286
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:110202579..110205350-chr3:110208750..110211546,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12054102	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13078633	0.90[CHB][hapmap]
rs1398346	0.86[CHD][hapmap]
rs1512662	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1606350	0.84[EUR][1000 genomes]
rs16856690	0.83[EUR][1000 genomes]
rs2055968	0.84[EUR][1000 genomes]
rs2895375	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57198450	0.83[EUR][1000 genomes]
rs57680282	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs58500543	1.00[EUR][1000 genomes]
rs59612531	0.83[EUR][1000 genomes]
rs59822825	0.83[EUR][1000 genomes]
rs59985710	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62269411	0.83[EUR][1000 genomes]
rs62269412	0.83[EUR][1000 genomes]
rs62269414	0.83[EUR][1000 genomes]
rs62269437	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62269438	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62269439	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62270060	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62270063	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62270076	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62270083	0.89[EUR][1000 genomes]
rs62270086	0.89[EUR][1000 genomes]
rs62270095	0.89[EUR][1000 genomes]
rs62270100	0.89[EUR][1000 genomes]
rs62270124	0.83[EUR][1000 genomes]
rs62270128	0.83[EUR][1000 genomes]
rs62270134	0.83[EUR][1000 genomes]
rs62271562	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62271576	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62271578	0.95[EUR][1000 genomes]
rs62271586	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62271587	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62271588	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62271591	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62271592	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62271606	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62271607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62271608	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62271609	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271610	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62271612	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271615	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271616	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271618	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62271620	0.89[EUR][1000 genomes]
rs62271621	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62271636	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271639	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271642	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271644	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62271646	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62271647	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6437914	0.90[EUR][1000 genomes]
rs6765569	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6781483	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6784411	0.83[EUR][1000 genomes]
rs6784648	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7617903	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628733	1.00[EUR][1000 genomes]
rs7631316	0.89[EUR][1000 genomes]
rs7634524	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7638452	0.89[ASN][1000 genomes]
rs9653909	0.89[EUR][1000 genomes]
rs9809312	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999414	chr3:110103126-110340180	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv829670	chr3:110134650-110308256	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv520365	chr3:110155172-110441165	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1001144	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv536687	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1001810	chr3:110158316-110522247	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1010230	chr3:110204439-110588814	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv536688	chr3:110204439-110588814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv829672	chr3:110206693-110361632	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1011034	chr3:110209344-110559021	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv536689	chr3:110209344-110559021	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16856946	DEFA1	trans	brain	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110209200-110211400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:110209800-110211000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:110210000-110210600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr3:110210000-110210800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:110210000-110211000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:110210000-110211000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:110210200-110210400	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:110210200-110211000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:110210200-110211000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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