Variant report

Variant	rs6064093
Chromosome Location	chr20:53241631-53241632
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53240556..53242975-chr20:53260288..53262063,2	MCF-7	breast:
2	chr20:53239460..53242242-chr20:53249088..53250613,2	MCF-7	breast:
3	chr20:53184698..53187233-chr20:53241070..53243919,2	MCF-7	breast:
4	chr20:53241214..53243048-chr20:53243529..53246350,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs13040265	1.00[CHD][hapmap]
rs1569985	1.00[CHD][hapmap]
rs16999872	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983702	1.00[CHD][hapmap]
rs2180462	1.00[CHD][hapmap]
rs2208075	1.00[CHD][hapmap];0.88[MEX][hapmap]
rs2224269	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[EUR][1000 genomes]
rs28663252	1.00[ASN][1000 genomes]
rs2870331	1.00[ASN][1000 genomes]
rs2870332	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs2870333	1.00[CHD][hapmap]
rs2870337	1.00[CHD][hapmap]
rs2904386	1.00[ASN][1000 genomes]
rs4302265	1.00[CHD][hapmap]
rs4324376	1.00[ASN][1000 genomes]
rs4334548	1.00[CHD][hapmap]
rs4542911	1.00[ASN][1000 genomes]
rs4581960	1.00[ASN][1000 genomes]
rs4809968	1.00[ASN][1000 genomes]
rs4809969	1.00[CHD][hapmap]
rs4811510	1.00[ASN][1000 genomes]
rs4811511	1.00[ASN][1000 genomes]
rs4811512	0.91[CEU][hapmap]
rs4811513	1.00[ASN][1000 genomes]
rs4996783	1.00[ASN][1000 genomes]
rs58298733	1.00[ASN][1000 genomes]
rs60030360	1.00[ASN][1000 genomes]
rs6014078	1.00[ASN][1000 genomes]
rs6014080	1.00[ASN][1000 genomes]
rs6014081	1.00[CHD][hapmap]
rs6014106	1.00[CHD][hapmap]
rs6023367	1.00[CHD][hapmap]
rs6023397	1.00[ASN][1000 genomes]
rs6023398	1.00[ASN][1000 genomes]
rs6023400	1.00[ASN][1000 genomes]
rs6023401	1.00[ASN][1000 genomes]
rs6023403	1.00[ASN][1000 genomes]
rs6023406	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6023408	1.00[ASN][1000 genomes]
rs6023409	1.00[ASN][1000 genomes]
rs6023410	1.00[ASN][1000 genomes]
rs6023423	1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs6023428	1.00[ASN][1000 genomes]
rs6023429	1.00[CHD][hapmap]
rs6023430	1.00[CHD][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs6023474	1.00[CHD][hapmap]
rs6064092	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6064102	1.00[CHD][hapmap]
rs6068916	1.00[ASN][1000 genomes]
rs6068919	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6068920	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6068923	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs6068924	1.00[CHD][hapmap];0.93[MEX][hapmap]
rs6091928	1.00[ASN][1000 genomes]
rs6091931	1.00[ASN][1000 genomes]
rs6098103	1.00[ASN][1000 genomes]
rs6098105	1.00[ASN][1000 genomes]
rs6098108	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6098120	1.00[ASN][1000 genomes]
rs6098158	1.00[CHD][hapmap]
rs6123404	1.00[CHD][hapmap]
rs7261209	1.00[ASN][1000 genomes]
rs7263678	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7263680	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7269966	1.00[ASN][1000 genomes]
rs7270451	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7270971	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs8115071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8124702	1.00[CHD][hapmap]
rs910850	1.00[CHD][hapmap]
rs967377	1.00[CHD][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6064093	RAE1	cis	cerebellum	SCAN
rs6064093	MOGS	trans	cerebellum	SCAN
rs6064093	SALL4	cis	cerebellum	SCAN
rs6064093	CASS4	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53235200-53250400	Weak transcription	Psoas Muscle	Psoas
2	chr20:53236000-53241800	Weak transcription	Pancreas	Pancrea
3	chr20:53236200-53250400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:53238400-53242000	Enhancers	Fetal Muscle Trunk	muscle
5	chr20:53238400-53242800	Enhancers	Fetal Muscle Leg	muscle
6	chr20:53238600-53242400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:53238800-53242400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr20:53238800-53242800	Enhancers	Fetal Lung	lung
9	chr20:53239200-53242000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:53239200-53242000	Enhancers	Brain Angular Gyrus	brain
11	chr20:53240400-53242000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr20:53240600-53242000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr20:53240600-53242400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr20:53240600-53242400	Enhancers	Fetal Kidney	kidney
15	chr20:53240600-53242400	Enhancers	Fetal Stomach	stomach
16	chr20:53240600-53242600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr20:53240800-53241800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr20:53240800-53241800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr20:53240800-53242800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr20:53240800-53245800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr20:53241000-53242200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr20:53241000-53242400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr20:53241000-53242400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr20:53241000-53246200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr20:53241200-53241800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr20:53241200-53241800	Active TSS	Brain Germinal Matrix	brain
27	chr20:53241200-53241800	Active TSS	Fetal Brain Female	brain
28	chr20:53241200-53242000	Enhancers	Brain Substantia Nigra	brain
29	chr20:53241200-53242200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr20:53241200-53242200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr20:53241200-53242400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr20:53241200-53242600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr20:53241400-53241800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr20:53241400-53241800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr20:53241400-53242400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr20:53241400-53248200	Weak transcription	NHDF-Ad	bronchial
37	chr20:53241400-53249800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:53241600-53241800	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr20:53241600-53241800	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr20:53241600-53241800	Flanking Active TSS	Fetal Brain Male	brain
41	chr20:53241600-53241800	Enhancers	NH-A	brain
42	chr20:53241600-53242000	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr20:53241600-53242400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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