Variant report

Variant	rs12656140
Chromosome Location	chr5:107314908-107314909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10037490	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056741	0.86[EUR][1000 genomes]
rs10077316	0.86[EUR][1000 genomes]
rs10515384	0.87[EUR][1000 genomes]
rs11739536	0.93[JPT][hapmap]
rs12054721	0.93[JPT][hapmap]
rs12514780	1.00[LWK][hapmap]
rs12651724	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs12651919	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12652687	0.92[TSI][hapmap]
rs12654751	0.86[CEU][hapmap]
rs12655573	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655932	1.00[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12657877	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12659666	0.80[EUR][1000 genomes]
rs13357987	0.80[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs1433057	0.93[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];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17437979	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17438307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439150	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]
rs17439877	0.89[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];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28670811	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4144476	0.80[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs4144478	0.87[EUR][1000 genomes]
rs4582260	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]
rs55780614	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55958078	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56108486	0.87[EUR][1000 genomes]
rs58342334	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58805667	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59356989	0.80[EUR][1000 genomes]
rs59606487	0.81[EUR][1000 genomes]
rs59711822	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59830006	0.80[EUR][1000 genomes]
rs60447697	0.87[EUR][1000 genomes]
rs6596766	0.87[EUR][1000 genomes]
rs6865057	0.81[EUR][1000 genomes]
rs6872913	0.87[EUR][1000 genomes]
rs723397	0.87[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73204759	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73204760	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73204762	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73204763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73204764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73204766	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73204790	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73204796	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73206507	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73206538	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7704251	0.90[EUR][1000 genomes]
rs7731562	0.80[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs7735773	0.80[MEX][hapmap];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
rs12656140	MAN2A1	cis	parietal	SCAN

Chromatin state (count:21 , 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	chr5:107302400-107334600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:107308400-107315400	Weak transcription	Fetal Lung	lung
4	chr5:107309000-107318800	Weak transcription	Left Ventricle	heart
5	chr5:107312400-107315200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:107312800-107317400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:107313400-107316200	Enhancers	Dnd41	blood
8	chr5:107313400-107317400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:107313600-107316200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:107313800-107315200	Weak transcription	Gastric	stomach
11	chr5:107313800-107315400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr5:107313800-107316800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:107313800-107318600	Weak transcription	Stomach Mucosa	stomach
14	chr5:107313800-107321000	Weak transcription	Lung	lung
15	chr5:107314000-107315400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:107314000-107316600	Weak transcription	Fetal Kidney	kidney
17	chr5:107314400-107320400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:107314600-107315000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:107314600-107315200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:107314600-107315400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr5:107314600-107320800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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