Variant report

Variant	rs17439150
Chromosome Location	chr5:107333402-107333403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107332693..107334247-chr5:107337068..107339147,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10037490	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10056741	0.89[EUR][1000 genomes]
rs10077316	0.89[EUR][1000 genomes]
rs10440792	0.81[EUR][1000 genomes]
rs10515384	0.90[EUR][1000 genomes]
rs11739536	0.93[JPT][hapmap]
rs12054721	0.93[JPT][hapmap]
rs12651724	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs12651919	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12652643	0.81[EUR][1000 genomes]
rs12652687	0.92[TSI][hapmap]
rs12654751	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs12655573	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12655932	0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12656140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12657877	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12659666	0.83[EUR][1000 genomes]
rs13357987	0.80[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs1433057	0.93[JPT][hapmap]
rs17381296	0.90[EUR][1000 genomes]
rs17382278	0.84[EUR][1000 genomes]
rs17383035	0.83[EUR][1000 genomes]
rs17384285	0.92[TSI][hapmap]
rs17437658	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17437979	0.81[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17438307	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17439877	0.93[EUR][1000 genomes]
rs17440508	0.90[EUR][1000 genomes]
rs17440818	0.90[EUR][1000 genomes]
rs17440916	0.90[EUR][1000 genomes]
rs17441920	0.83[EUR][1000 genomes]
rs17442211	0.83[EUR][1000 genomes]
rs2042187	0.90[EUR][1000 genomes]
rs2067765	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28670811	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4144476	0.80[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4144478	0.90[EUR][1000 genomes]
rs4582260	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55780614	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55958078	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56108486	0.90[EUR][1000 genomes]
rs58342334	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58805667	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59356989	0.83[EUR][1000 genomes]
rs59606487	0.84[EUR][1000 genomes]
rs59711822	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59830006	0.83[EUR][1000 genomes]
rs60447697	0.90[EUR][1000 genomes]
rs6596766	0.91[EUR][1000 genomes]
rs6864731	0.81[EUR][1000 genomes]
rs6865057	0.84[EUR][1000 genomes]
rs6872913	0.90[EUR][1000 genomes]
rs723397	0.87[CEU][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73204759	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73204760	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73204762	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73204763	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73204764	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73204766	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73204790	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73204796	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73206507	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73206538	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7704251	0.93[EUR][1000 genomes]
rs7731562	0.80[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7735773	0.80[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][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	nsv882682	chr5:107213361-107458336	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17439150	MAN2A1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107302400-107334600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:107319800-107354000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:107321200-107338800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:107327400-107353400	Weak transcription	Aorta	Aorta
5	chr5:107332600-107333800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr5:107332600-107333800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:107332600-107334000	Enhancers	H9 Cell Line	embryonic stem cell
8	chr5:107332600-107334200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:107332800-107333800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr5:107332800-107334000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:107332800-107334000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:107333000-107333600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:107333000-107333600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:107333000-107333600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:107333000-107333800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:107333000-107333800	Enhancers	Fetal Brain Male	brain
17	chr5:107333200-107333600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:107333200-107333600	Enhancers	Fetal Brain Female	brain
19	chr5:107333200-107333600	Enhancers	HSMMtube	muscle
20	chr5:107333200-107333800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:107333200-107333800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:107333200-107333800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:107333200-107333800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:107333200-107333800	Enhancers	Osteobl	bone
25	chr5:107333400-107333600	Flanking Active TSS	HUVEC	blood vessel
26	chr5:107333400-107333800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:107333400-107333800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr5:107333400-107333800	Enhancers	NHDF-Ad	bronchial
29	chr5:107333400-107336400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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