Variant report

Variant	rs566841
Chromosome Location	chr1:166628002-166628003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:166606674..166608700-chr1:166627422..166629735,2	MCF-7	breast:
2	chr1:166624683..166630041-chr1:166630762..166637027,8	K562	blood:

Variant related genes	Relation type
ENSG00000234984	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10047082	0.97[ASN][1000 genomes]
rs10494466	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10800253	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10800256	0.84[ASN][1000 genomes]
rs10918553	0.91[ASN][1000 genomes]
rs10918554	0.97[ASN][1000 genomes]
rs11585016	0.97[ASN][1000 genomes]
rs12022093	0.83[AMR][1000 genomes]
rs12022833	0.95[ASN][1000 genomes]
rs12032695	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12074816	0.86[ASN][1000 genomes]
rs12074860	0.86[ASN][1000 genomes]
rs12082938	0.97[ASN][1000 genomes]
rs12406568	0.97[ASN][1000 genomes]
rs1631056	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17472904	0.86[ASN][1000 genomes]
rs3125820	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34311259	0.87[ASN][1000 genomes]
rs3904697	0.81[ASN][1000 genomes]
rs3904700	0.86[ASN][1000 genomes]
rs3904701	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4068473	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4090281	0.97[ASN][1000 genomes]
rs4320765	0.84[ASN][1000 genomes]
rs4393133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4475724	0.82[AFR][1000 genomes]
rs4514220	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs471764	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs473746	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs474189	0.80[LWK][hapmap];0.83[MKK][hapmap]
rs475264	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs482782	0.86[ASN][1000 genomes]
rs482850	0.86[ASN][1000 genomes]
rs482905	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs483138	0.84[ASN][1000 genomes]
rs484070	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs496095	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs500437	0.82[ASN][1000 genomes]
rs500568	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs503960	0.84[ASN][1000 genomes]
rs505012	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs505135	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs511809	0.84[ASN][1000 genomes]
rs514307	0.84[ASN][1000 genomes]
rs519135	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs524397	0.86[ASN][1000 genomes]
rs525948	0.80[ASN][1000 genomes]
rs527241	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs529740	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs530513	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs530690	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs532412	0.84[ASN][1000 genomes]
rs535889	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs536773	0.86[ASN][1000 genomes]
rs537720	0.81[ASN][1000 genomes]
rs537782	0.84[ASN][1000 genomes]
rs542999	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs552888	0.82[MKK][hapmap]
rs553928	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs556269	0.80[ASN][1000 genomes]
rs558874	0.82[MKK][hapmap]
rs563206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs568776	0.84[ASN][1000 genomes]
rs568821	0.84[ASN][1000 genomes]
rs571669	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs579545	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs580432	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7523559	0.84[ASN][1000 genomes]
rs7530194	0.84[ASN][1000 genomes]
rs7539202	0.91[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.83[TSI][hapmap]
rs7540624	0.84[ASN][1000 genomes]

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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv2757759	chr1:166491879-166650985	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2758975	chr1:166491879-166650985	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2752389	chr1:166625342-166706342	Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs566841	C1orf192	cis	parietal	SCAN
rs566841	ADCY10	cis	cerebellum	SCAN
rs566841	HNF1B	trans	lymphoblastoid	seeQTL
rs566841	MMP7	trans	lymphoblastoid	seeQTL
rs566841	MTTP	trans	lymphoblastoid	seeQTL

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

No data

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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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