Variant report

Variant	rs4659245
Chromosome Location	chr1:120415986-120415987
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120283662..120285685-chr1:120414247..120416692,2	MCF-7	breast:
2	chr1:120356024..120358010-chr1:120414554..120416804,2	MCF-7	breast:
3	chr1:120414299..120416081-chr1:120419114..120421121,2	MCF-7	breast:
4	chr1:120415380..120417252-chr1:120419705..120421927,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10802138	0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10923918	0.88[ASN][1000 genomes]
rs10923921	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17258579	1.00[YRI][hapmap]
rs2641337	0.84[ASN][1000 genomes]
rs4659247	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv533996	chr1:120359524-120471049	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv436325	chr1:120390914-120471049	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4659245	MON1A	trans	cerebellum	SCAN
rs4659245	WDR3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120409600-120416000	Weak transcription	Fetal Lung	lung
2	chr1:120413400-120417200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:120413600-120417000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:120413800-120417200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:120413800-120417200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:120413800-120417200	Enhancers	HSMM	muscle
7	chr1:120413800-120417200	Enhancers	NHDF-Ad	bronchial
8	chr1:120413800-120417200	Enhancers	NHLF	lung
9	chr1:120413800-120417600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:120414200-120416400	Weak transcription	Adipose Nuclei	Adipose
11	chr1:120414200-120416800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:120414200-120417200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:120414200-120417200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:120414200-120417200	Enhancers	Osteobl	bone
15	chr1:120414200-120419600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr1:120414400-120417000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:120414600-120419800	Weak transcription	Dnd41	blood
18	chr1:120415000-120417000	Enhancers	Fetal Kidney	kidney
19	chr1:120415000-120417200	Enhancers	Colon Smooth Muscle	Colon
20	chr1:120415000-120417200	Enhancers	Fetal Muscle Leg	muscle
21	chr1:120415200-120416000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:120415200-120417000	Enhancers	Fetal Heart	heart
23	chr1:120415200-120417200	Enhancers	Fetal Stomach	stomach
24	chr1:120415200-120417200	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:120415200-120417200	Enhancers	Stomach Smooth Muscle	stomach
26	chr1:120415200-120417200	Enhancers	HMEC	breast
27	chr1:120415200-120417200	Enhancers	NH-A	brain
28	chr1:120415400-120417200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:120415400-120417200	Enhancers	HSMMtube	muscle
30	chr1:120415400-120417600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:120415600-120417200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr1:120415800-120417200	Enhancers	Right Atrium	heart
33	chr1:120415800-120417600	Enhancers	K562	blood

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