Variant report

Variant	rs9988431
Chromosome Location	chr1:86457375-86457376
allele	A/G
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:20)

rs_ID	r²[population]
rs12723976	0.81[EUR][1000 genomes]
rs12725994	0.82[EUR][1000 genomes]
rs12736258	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs12736520	0.81[EUR][1000 genomes]
rs12740195	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs12742014	0.84[EUR][1000 genomes]
rs12754643	0.85[EUR][1000 genomes]
rs12755069	0.83[EUR][1000 genomes]
rs12756057	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs1393554	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs1998684	0.80[CEU][hapmap];0.89[EUR][1000 genomes]
rs35982302	0.85[EUR][1000 genomes]
rs476149	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs541395	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs555289	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs566108	0.86[EUR][1000 genomes]
rs598471	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs676973	0.89[YRI][hapmap]
rs689040	0.86[EUR][1000 genomes]
rs71506583	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv546758	chr1:86438327-86483632	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3340591	chr1:86439980-86459810	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1012808	chr1:86455710-86470489	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86449400-86466200	Weak transcription	Fetal Lung	lung
2	chr1:86454400-86458200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:86456200-86457600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:86456200-86464600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:86456400-86457400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:86457000-86458800	Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr1:86457000-86458800	Active TSS	GM12878-XiMat	blood
8	chr1:86457200-86457400	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:86457200-86457400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:86457200-86459800	Weak transcription	Dnd41	blood

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