Variant report

Variant	rs12126310
Chromosome Location	chr1:160886563-160886564
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160850486..160853249-chr1:160886390..160887944,2	K562	blood:

Variant related genes	Relation type
ENSG00000179914	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10908810	0.82[AFR][1000 genomes]
rs11265510	0.81[JPT][hapmap];0.85[MEX][hapmap]
rs11265522	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265526	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265533	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11265534	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11587040	0.85[MEX][hapmap]
rs11805631	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12135639	0.83[AFR][1000 genomes]
rs1855186	0.90[MEX][hapmap]
rs1855187	0.81[JPT][hapmap]
rs1981048	0.80[AMR][1000 genomes]
rs2039415	0.85[MEX][hapmap]
rs2184066	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274908	0.81[LWK][hapmap]
rs2274910	0.88[LWK][hapmap];0.80[MEX][hapmap]
rs28368883	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34655593	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3766356	0.83[YRI][hapmap]
rs3829790	0.85[CHB][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3928803	0.81[EUR][1000 genomes]
rs4656958	0.85[MEX][hapmap]
rs4656968	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656971	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4656972	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61802165	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6656769	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6680969	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6691389	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7411035	0.81[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap]
rs7516660	0.85[MEX][hapmap]
rs7526396	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs955615	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv3430322	chr1:160851829-160920480	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv947200	chr1:160870136-160905390	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12126310	F11R	cis	parietal	SCAN
rs12126310	RP11-312J18.6	cis	Thyroid	GTEx
rs12126310	LMNA	cis	parietal	SCAN
rs12126310	C1orf110	cis	cerebellum	SCAN
rs12126310	USP21	cis	cerebellum	SCAN
rs12126310	SPTA1	cis	parietal	SCAN
rs12126310	APCS	cis	cerebellum	SCAN
rs12126310	ARHGAP30	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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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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