Variant report

Variant	rs2256504
Chromosome Location	chr7:103165895-103165896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10248053	0.91[CEU][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap]
rs10278964	0.82[CHD][hapmap]
rs1062831	0.82[CHD][hapmap]
rs17151768	0.82[CHD][hapmap]
rs2256512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2256658	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2256670	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2528866	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs2711864	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3808033	0.91[CEU][hapmap]
rs3823992	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv831085	chr7:103140672-103342388	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv888923	chr7:103143117-103199719	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2256504	ATXN7L1	cis	parietal	SCAN
rs2256504	OR2AE1	cis	parietal	SCAN
rs2256504	SLC26A5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103158000-103198600	Weak transcription	Liver	Liver
2	chr7:103161000-103168000	Weak transcription	HepG2	liver
3	chr7:103162800-103168000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:103163600-103166000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr7:103164600-103166000	Enhancers	Fetal Heart	heart
6	chr7:103165000-103179200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:103165200-103173000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:103165600-103169600	Weak transcription	K562	blood
9	chr7:103165800-103166200	Weak transcription	Brain Substantia Nigra	brain

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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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