Variant report

Variant	rs13243127
Chromosome Location	chr7:78072997-78072998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10264526	0.83[CHB][hapmap]
rs10264753	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10485887	0.83[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs11760299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11765817	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[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];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11767536	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11767605	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12670044	1.00[YRI][hapmap]
rs1861383	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1861384	0.96[ASN][1000 genomes]
rs2110871	0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.80[ASN][1000 genomes]
rs2110873	1.00[YRI][hapmap]
rs34058977	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34896695	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6957462	0.83[CHB][hapmap]
rs6961316	0.83[CHB][hapmap]
rs7784064	0.84[CEU][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7788384	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13243127	PHTF2	cis	parietal	SCAN
rs13243127	GTF2IRD1	cis	cerebellum	SCAN
rs13243127	RPL13AP17	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78067000-78079800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:78071000-78073600	Enhancers	Brain Anterior Caudate	brain
3	chr7:78071400-78073000	Enhancers	Brain Substantia Nigra	brain
4	chr7:78071400-78073600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr7:78071600-78073200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:78072200-78073200	Enhancers	Fetal Heart	heart
7	chr7:78072400-78073200	Enhancers	Brain Cingulate Gyrus	brain
8	chr7:78072800-78077400	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:78072800-78079600	Weak transcription	Brain Angular Gyrus	brain
10	chr7:78072800-78079800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

Quick Search:

Input of quick search could be:

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

what's new

Quick links