Variant report

Variant	rs1531836
Chromosome Location	chr4:53850860-53850861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10010254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133240	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13104612	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104971	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs13120717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123449	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13134756	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1319626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384695	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2170689	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898683	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs301089	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301110	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs301112	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34704735	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3849652	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs403536	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554062	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554063	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831230	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6844522	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6853639	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7685087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689426	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs958693	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv508280	chr4:53825060-53907661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1531836	NMU	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53786600-53861400	Weak transcription	Primary B cells from cord blood	blood
2	chr4:53847400-53851200	Enhancers	Fetal Kidney	kidney
3	chr4:53848000-53851400	Enhancers	NHDF-Ad	bronchial
4	chr4:53848000-53851600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:53848600-53851200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:53849200-53851400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:53849200-53851600	Enhancers	Fetal Stomach	stomach
8	chr4:53849600-53851000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:53850000-53851000	Enhancers	HepG2	liver
10	chr4:53850000-53851000	Enhancers	HMEC	breast
11	chr4:53850000-53851000	Enhancers	NHLF	lung
12	chr4:53850000-53851200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:53850000-53851200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr4:53850000-53851200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:53850000-53851200	Enhancers	Colon Smooth Muscle	Colon
16	chr4:53850000-53851200	Enhancers	Osteobl	bone
17	chr4:53850000-53851600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:53850000-53851600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:53850000-53851600	Enhancers	Fetal Lung	lung
20	chr4:53850200-53851200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:53850200-53851600	Enhancers	Ovary	ovary
22	chr4:53850400-53860000	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:53850400-53864600	Weak transcription	Primary T cells from cord blood	blood
24	chr4:53850400-53869600	Weak transcription	GM12878-XiMat	blood
25	chr4:53850600-53851200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:53850800-53853600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:53850800-53853600	Weak transcription	Fetal Heart	heart

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