Variant report

Variant	rs2239279
Chromosome Location	chr14:72938057-72938058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2238184	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2239213	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2239280	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2283379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819547	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs7151951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs735995	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8008067	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs8014634	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2239279	RDH12	cis	cerebellum	SCAN
rs2239279	SMOC1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72919400-72945200	Weak transcription	Brain Germinal Matrix	brain
2	chr14:72923800-72946200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:72930200-72943400	Weak transcription	Left Ventricle	heart
4	chr14:72930400-72943000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:72933800-72942000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr14:72934400-72943400	Weak transcription	Spleen	Spleen
7	chr14:72935600-72941600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr14:72936000-72946200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr14:72936800-72940200	Weak transcription	Fetal Brain Female	brain
10	chr14:72937600-72943000	Weak transcription	Fetal Muscle Leg	muscle
11	chr14:72938000-72938400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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