Variant report

Variant	rs13427344
Chromosome Location	chr2:98948224-98948225
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98947397..98949375-chr2:98973131..98975837,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10172281	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10181000	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190679	0.98[ASN][1000 genomes]
rs10199476	0.87[CHB][hapmap]
rs10201994	0.89[AMR][1000 genomes]
rs10210685	0.98[ASN][1000 genomes]
rs11124096	0.87[CHB][hapmap]
rs11124107	0.87[CHB][hapmap]
rs11673807	0.87[CHB][hapmap]
rs11679920	0.87[CHB][hapmap]
rs11889349	0.87[CHB][hapmap];0.81[TSI][hapmap]
rs11895654	0.87[CHB][hapmap]
rs12478763	0.87[CHB][hapmap]
rs12622324	0.87[CHB][hapmap]
rs12999985	0.87[CHB][hapmap]
rs13014142	0.87[CHB][hapmap]
rs13394706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13408372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13428221	0.91[ASN][1000 genomes]
rs13432099	0.98[ASN][1000 genomes]
rs1451251	0.93[CHB][hapmap]
rs1466944	0.87[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1546351	0.84[YRI][hapmap]
rs17429208	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055591	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2102270	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2122756	0.87[CHB][hapmap]
rs2202387	0.87[CHB][hapmap]
rs2221416	0.87[CHB][hapmap];0.81[TSI][hapmap]
rs2292118	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292119	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[YRI][hapmap]
rs3769755	0.80[CHB][hapmap]
rs4374424	0.87[CHB][hapmap]
rs4455212	0.92[CHB][hapmap]
rs4477970	0.87[CHB][hapmap]
rs4479470	0.87[CHB][hapmap]
rs4608580	0.87[CHB][hapmap]
rs4632400	0.87[CHB][hapmap]
rs4851935	0.87[CHB][hapmap]
rs4851951	0.92[CHB][hapmap]
rs4851959	0.84[EUR][1000 genomes]
rs4851960	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56320609	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs60924437	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62156263	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62156264	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6543419	0.87[CHB][hapmap]
rs66464436	0.84[EUR][1000 genomes]
rs6715989	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs6725543	0.87[CHB][hapmap]
rs6742930	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6747344	0.87[CHB][hapmap]
rs6747410	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6754222	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72819909	0.98[ASN][1000 genomes]
rs7571001	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7571110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578802	0.87[CHB][hapmap]
rs7580008	1.00[ASN][1000 genomes]
rs7586663	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589018	0.84[EUR][1000 genomes]
rs7601049	0.87[CHB][hapmap]
rs7606220	0.87[CHB][hapmap]

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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13427344	NEUROG3	trans	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98940600-98949400	Weak transcription	Osteobl	bone
2	chr2:98946800-98948800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:98946800-98950400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:98947000-98948400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:98947800-98949200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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