Variant report

Variant	rs9850978
Chromosome Location	chr3:61187274-61187275
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11130829	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11711523	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11714760	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320670	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28584187	0.86[ASN][1000 genomes]
rs28649296	0.86[ASN][1000 genomes]
rs28738855	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2886261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34253135	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62267451	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62267453	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268422	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268813	0.86[ASN][1000 genomes]
rs9815151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816826	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9845924	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv997718	chr3:61176349-61222975	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61151200-61188000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61172400-61203000	Weak transcription	Pancreas	Pancrea
3	chr3:61185600-61187600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:61186000-61189000	Enhancers	Primary hematopoietic stem cells	blood
5	chr3:61186000-61195600	Weak transcription	Fetal Intestine Small	intestine
6	chr3:61187000-61187400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:61187000-61189200	Enhancers	GM12878-XiMat	blood
8	chr3:61187200-61187400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:61187200-61188000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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