Variant report

Variant	rs4640664
Chromosome Location	chr4:86932486-86932487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10009993	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10028075	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1010778	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10856856	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11934691	0.83[ASN][1000 genomes]
rs12644938	0.85[ASN][1000 genomes]
rs12644947	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1436527	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2589506	0.83[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs2589514	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2589515	0.83[AMR][1000 genomes]
rs2589516	0.83[AMR][1000 genomes]
rs3775181	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3775183	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3775187	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4133139	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4482754	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4487330	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6531896	0.85[ASN][1000 genomes]
rs6810413	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7692676	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4640664	LIN54	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
2	chr4:86916800-86935800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:86916800-86985400	Weak transcription	Ovary	ovary
4	chr4:86917000-86933800	Weak transcription	Gastric	stomach
5	chr4:86917000-86933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:86917000-86935200	Weak transcription	Left Ventricle	heart
7	chr4:86917000-86935800	Weak transcription	Spleen	Spleen
8	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
9	chr4:86917400-86940400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:86919400-86941200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:86920200-86933800	Weak transcription	Aorta	Aorta
12	chr4:86922800-86935200	Weak transcription	Right Atrium	heart
13	chr4:86925400-86937200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:86925600-86935000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:86925600-86935200	Weak transcription	Adipose Nuclei	Adipose
16	chr4:86925600-86935600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr4:86925600-86937400	Weak transcription	Fetal Kidney	kidney
18	chr4:86927400-86935400	Weak transcription	Primary B cells from cord blood	blood
19	chr4:86928400-86937800	Weak transcription	Fetal Stomach	stomach
20	chr4:86928600-86953400	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:86931000-86935200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:86931600-86933200	Enhancers	NHDF-Ad	bronchial
23	chr4:86931600-86937600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:86931800-86932600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:86931800-86932800	Enhancers	NH-A	brain
26	chr4:86931800-86933000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:86931800-86933200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:86931800-86933600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:86931800-86937600	Enhancers	Osteobl	bone
30	chr4:86932000-86932600	Enhancers	HUVEC	blood vessel
31	chr4:86932000-86932800	Enhancers	NHLF	lung
32	chr4:86932200-86932600	Enhancers	HSMMtube	muscle
33	chr4:86932200-86932800	Enhancers	HMEC	breast
34	chr4:86932200-86934000	Enhancers	Fetal Heart	heart
35	chr4:86932400-86932600	Enhancers	Brain Angular Gyrus	brain
36	chr4:86932400-86932600	Enhancers	Right Ventricle	heart
37	chr4:86932400-86932800	Enhancers	Fetal Lung	lung
38	chr4:86932400-86933000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:86932400-86933200	Enhancers	HSMM	muscle
40	chr4:86932400-86935200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:86932400-86935800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:86932400-86937600	Weak transcription	Brain Inferior Temporal Lobe	brain

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