Variant report

Variant	rs7144427
Chromosome Location	chr14:78773933-78773934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11159350	0.83[CHD][hapmap]
rs12432856	1.00[ASW][hapmap]
rs13329054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523131	0.83[CHD][hapmap]
rs17755949	0.82[ASW][hapmap]
rs1882812	0.83[CHD][hapmap]
rs2205163	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2205164	0.83[CHD][hapmap]
rs4903742	0.83[CHD][hapmap]
rs4903743	1.00[YRI][hapmap]
rs7149016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152608	0.88[YRI][hapmap]
rs8018121	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8018122	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8018257	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8021038	0.83[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs986980	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][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	nsv832837	chr14:78766805-78946526	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1054051	chr14:78772614-78805311	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7144427	JDP2	cis	cerebellum	SCAN
rs7144427	ACOT1	cis	parietal	SCAN
rs7144427	TMED10	cis	cerebellum	SCAN
rs7144427	TSHR	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78738600-78778200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr14:78738600-78779000	Weak transcription	Brain Angular Gyrus	brain
3	chr14:78750200-78778400	Weak transcription	Brain Anterior Caudate	brain
4	chr14:78769000-78774000	Enhancers	Brain Germinal Matrix	brain
5	chr14:78769200-78783200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:78772800-78774600	Enhancers	Fetal Brain Male	brain
7	chr14:78772800-78774800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr14:78773000-78775400	Enhancers	Fetal Brain Female	brain
9	chr14:78773800-78775200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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