Variant report

Variant	rs6750246
Chromosome Location	chr2:48271125-48271126
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10167776	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10196696	0.96[ASN][1000 genomes]
rs10865228	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11125157	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1471680	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1471681	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1473611	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1483210	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1483215	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1483221	0.86[ASN][1000 genomes]
rs17324704	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1825320	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1878079	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1878081	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2056138	0.98[ASN][1000 genomes]
rs2128716	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2128718	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28460586	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4146021	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952901	0.86[ASN][1000 genomes]
rs4952904	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4953534	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4953544	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953546	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4953549	0.83[EUR][1000 genomes]
rs4953555	0.86[CEU][hapmap]
rs6545011	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545017	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545019	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6706664	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6712238	0.82[EUR][1000 genomes]
rs6720994	0.94[ASN][1000 genomes]
rs6723952	0.83[EUR][1000 genomes]
rs6749276	1.00[ASN][1000 genomes]
rs6759902	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7563749	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7584401	0.96[ASN][1000 genomes]
rs7584493	1.00[ASN][1000 genomes]
rs7609066	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7609124	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs900506	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs900510	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs900511	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs922902	0.91[CEU][hapmap]
rs963133	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs963135	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs968888	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs999036	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv874000	chr2:48078838-48291582	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv833969	chr2:48220927-48328328	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6750246	FOXN2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48270200-48271400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:48270200-48272200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:48270200-48272800	Enhancers	Placenta	Placenta
4	chr2:48270400-48271200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr2:48270400-48271800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:48270800-48275600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:48271000-48271800	Active TSS	K562	blood

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