Variant report

Variant	rs1897725
Chromosome Location	chr9:18866563-18866564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10756995	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1433830	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2099392	1.00[JPT][hapmap]
rs6475268	0.82[ASN][1000 genomes]
rs7029205	0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7032286	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7032557	0.83[ASN][1000 genomes]
rs7047294	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7864844	0.81[JPT][hapmap]
rs7875400	0.81[CEU][hapmap]
rs7875489	0.83[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	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892698	chr9:18830444-18905289	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1897725	PTPLAD2	cis	parietal	SCAN
rs1897725	MTAP	cis	cerebellum	SCAN
rs1897725	IFNB1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18858800-18876600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:18862400-18866800	Weak transcription	Right Ventricle	heart
3	chr9:18862800-18870000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:18863000-18871200	Strong transcription	HSMM	muscle
5	chr9:18863800-18881800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:18864400-18868200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:18864400-18868800	Weak transcription	Aorta	Aorta
8	chr9:18864400-18883000	Weak transcription	NH-A	brain
9	chr9:18864800-18869000	Weak transcription	Fetal Stomach	stomach
10	chr9:18865000-18868800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:18865000-18869200	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:18865600-18867200	Enhancers	Osteobl	bone
13	chr9:18866000-18868800	Weak transcription	NHDF-Ad	bronchial
14	chr9:18866000-18869200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:18866200-18866800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:18866400-18867000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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

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