Variant report

Variant	rs11164042
Chromosome Location	chr1:76178440-76178441
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	chr1:76177430..76180048-chr1:76194109..76196652,2	K562	blood:
2	chr1:76178176..76179962-chr1:76184780..76186701,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1001160	0.88[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs10873797	0.88[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs11161699	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11161848	0.88[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs11163904	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11163915	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11163967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146631	1.00[JPT][hapmap]
rs1146634	1.00[JPT][hapmap]
rs1146636	1.00[JPT][hapmap]
rs1146644	1.00[JPT][hapmap]
rs11576534	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11578480	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11579752	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584577	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11588643	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1159215	0.88[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs11810154	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12118229	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12118306	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12125933	0.94[EUR][1000 genomes]
rs12126155	0.94[EUR][1000 genomes]
rs12129523	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12130334	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12130832	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12131344	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12131493	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12132503	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12132750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12138018	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142247	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12145870	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1250876	0.96[CEU][hapmap]
rs1250880	0.92[CEU][hapmap]
rs1303870	0.88[CEU][hapmap]
rs1463812	1.00[JPT][hapmap]
rs1498311	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17585530	0.94[EUR][1000 genomes]
rs17647178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17647711	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17848068	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1846233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1856791	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1908089	0.88[CEU][hapmap]
rs2029682	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2147039	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4403585	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4646960	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57249318	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5745323	1.00[JPT][hapmap]
rs5745325	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5745331	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5745347	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5745383	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5745394	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5745430	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs5745523	0.88[CEU][hapmap]
rs5745543	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs5745545	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs5745546	0.88[CEU][hapmap]
rs5745547	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs60550898	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656501	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6664254	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6675212	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687882	0.80[CEU][hapmap]
rs6704444	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs721204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs72979226	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74090722	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74090730	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516477	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv871572	chr1:76161889-76208488	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11164042	SNORD45B	cis	cerebellum	SCAN
rs11164042	SNORD45B	cis	parietal	SCAN
rs11164042	PIGK	cis	parietal	SCAN
rs11164042	RABGGTB	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76177000-76178600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:76177400-76178800	Enhancers	Stomach Smooth Muscle	stomach
3	chr1:76177600-76179000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:76177800-76178600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:76178400-76178800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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