Variant report

Variant	rs4680382
Chromosome Location	chr3:157324261-157324262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:157324181..157324705-chr3:157417909..157418475,2	MCF-7	breast:
2	chr10:71668806..71669307-chr3:157324109..157324687,3	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11914492	0.91[EUR][1000 genomes]
rs12696052	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1392185	0.89[EUR][1000 genomes]
rs1463853	0.89[EUR][1000 genomes]
rs1499781	0.89[EUR][1000 genomes]
rs1499782	0.89[EUR][1000 genomes]
rs4261829	0.90[EUR][1000 genomes]
rs4395360	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs4472012	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs4502543	0.90[ASN][1000 genomes]
rs4596103	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680383	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792250	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6804583	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289986	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs9289987	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9289989	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812718	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap]
rs9817096	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs9837954	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9838074	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs9870015	0.84[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829767	chr3:157306411-157490444	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv4081	chr3:157318466-157347655	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4680382	ARL14	cis	parietal	SCAN
rs4680382	LXN	cis	parietal	SCAN
rs4680382	GMPS	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157323400-157324400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:157323400-157324800	Enhancers	Fetal Brain Male	brain
3	chr3:157323600-157325600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:157323800-157324800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:157323800-157325800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:157323800-157326200	Enhancers	Brain Germinal Matrix	brain
7	chr3:157324000-157324400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:157324000-157324400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:157324000-157324400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:157324000-157324400	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:157324000-157324400	Enhancers	Osteobl	bone
12	chr3:157324000-157324800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:157324000-157324800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:157324000-157324800	Enhancers	Brain Anterior Caudate	brain
15	chr3:157324000-157324800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:157324000-157326600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:157324200-157324400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:157324200-157324400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:157324200-157324400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:157324200-157324400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:157324200-157324400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:157324200-157324400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:157324200-157324400	Enhancers	Brain Substantia Nigra	brain
24	chr3:157324200-157324600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:157324200-157324600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:157324200-157324600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:157324200-157324600	Enhancers	Fetal Muscle Leg	muscle
28	chr3:157324200-157324600	Enhancers	Stomach Mucosa	stomach
29	chr3:157324200-157324800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:157324200-157324800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:157324200-157324800	Enhancers	Adipose Nuclei	Adipose
32	chr3:157324200-157324800	Enhancers	Liver	Liver
33	chr3:157324200-157325200	Enhancers	Primary hematopoietic stem cells	blood

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