Variant report

Variant	rs4582260
Chromosome Location	chr5:107308944-107308945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10037490	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10056741	0.82[EUR][1000 genomes]
rs10077316	0.82[EUR][1000 genomes]
rs10515384	0.87[EUR][1000 genomes]
rs11739536	0.85[JPT][hapmap]
rs12054721	0.85[JPT][hapmap]
rs12651724	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs12651919	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12652687	0.92[TSI][hapmap]
rs12654751	0.86[CEU][hapmap]
rs12655573	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12655932	0.81[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs12656140	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12657877	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12659666	0.80[EUR][1000 genomes]
rs13357987	0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs1433057	0.85[JPT][hapmap]
rs17381296	0.87[EUR][1000 genomes]
rs17382278	0.81[EUR][1000 genomes]
rs17383035	0.80[EUR][1000 genomes]
rs17384285	0.92[TSI][hapmap]
rs17437658	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17437979	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17438307	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17439150	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]
rs17439877	0.85[EUR][1000 genomes]
rs17440508	0.87[EUR][1000 genomes]
rs17440818	0.87[EUR][1000 genomes]
rs17440916	0.87[EUR][1000 genomes]
rs17441920	0.80[EUR][1000 genomes]
rs17442211	0.80[EUR][1000 genomes]
rs2042187	0.87[EUR][1000 genomes]
rs2067765	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28670811	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144476	0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs4144478	0.87[EUR][1000 genomes]
rs55780614	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55958078	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56108486	0.87[EUR][1000 genomes]
rs58342334	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58805667	0.86[EUR][1000 genomes]
rs59356989	0.80[EUR][1000 genomes]
rs59606487	0.81[EUR][1000 genomes]
rs59711822	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59830006	0.80[EUR][1000 genomes]
rs60447697	0.87[EUR][1000 genomes]
rs6596766	0.83[EUR][1000 genomes]
rs6865057	0.81[EUR][1000 genomes]
rs6872913	0.87[EUR][1000 genomes]
rs723397	0.87[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73204759	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73204760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73204762	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73204763	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73204764	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73204766	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73204790	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73204796	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73206507	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73206538	0.86[EUR][1000 genomes]
rs7704251	0.86[EUR][1000 genomes]
rs7731562	0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7735773	0.92[TSI][hapmap];0.87[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
rs4582260	MAN2A1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107296200-107321000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:107302200-107310400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:107302400-107309400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:107302400-107313800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:107302400-107334600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:107303200-107309200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:107304200-107314200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:107305000-107313400	Weak transcription	Gastric	stomach
9	chr5:107305200-107310000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:107305400-107313600	Weak transcription	NHEK	skin
11	chr5:107307000-107310000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:107307000-107310600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:107307600-107309800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:107308400-107315400	Weak transcription	Fetal Lung	lung
15	chr5:107308600-107309000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:107308600-107309000	Enhancers	Left Ventricle	heart
17	chr5:107308600-107309400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:107308800-107309000	Weak transcription	Esophagus	oesophagus
19	chr5:107308800-107309000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr5:107308800-107309800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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