Variant report

Variant	rs149683
Chromosome Location	chr14:72623890-72623891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10142058	0.84[ASW][hapmap];0.81[CEU][hapmap];0.80[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap]
rs10148272	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs11628641	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs12432254	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs149672	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs149675	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs149676	0.96[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8004977	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs8005777	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs8009180	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9323565	0.95[CHB][hapmap];0.90[JPT][hapmap];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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv902076	chr14:72565656-72632217	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv902077	chr14:72576679-72632217	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv902078	chr14:72581575-72628433	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv902079	chr14:72583802-72632217	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv902080	chr14:72587872-72632217	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1041759	chr14:72612882-72628815	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs149683	YLPM1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72620400-72633400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72623400-72624200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr14:72623600-72624800	Weak transcription	Left Ventricle	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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