Variant report

Variant	rs1846233
Chromosome Location	chr1:76159354-76159355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76157193..76160004-chr1:76260955..76264534,3	K562	blood:
2	chr1:76158085..76160004-chr1:76262153..76264534,2	K562	blood:
3	chr1:76153507..76155716-chr1:76158535..76161147,2	K562	blood:
4	chr1:76139328..76142229-chr1:76158809..76161190,2	K562	blood:
5	chr1:76157340..76160559-chr1:76189001..76191132,3	K562	blood:
6	chr1:76158932..76160525-chr1:76160690..76162510,2	K562	blood:

Variant related genes	Relation type
ENSG00000057468	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1001160	0.88[CEU][hapmap];0.90[GIH][hapmap];0.80[TSI][hapmap]
rs11163904	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11163915	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11163967	1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164042	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11576534	0.84[EUR][1000 genomes]
rs11578480	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11579752	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11584577	0.84[EUR][1000 genomes]
rs11586638	0.81[EUR][1000 genomes]
rs11588643	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11589276	0.82[EUR][1000 genomes]
rs1159215	0.88[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap]
rs11810154	0.84[EUR][1000 genomes]
rs12118229	0.84[EUR][1000 genomes]
rs12118306	0.84[EUR][1000 genomes]
rs12125933	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12126155	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12129523	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12130334	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12130832	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][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[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12131493	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12132503	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12132750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12138018	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12142247	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12145870	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1250876	0.96[CEU][hapmap]
rs1250880	0.92[CEU][hapmap]
rs1498311	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs17585530	0.96[EUR][1000 genomes]
rs17647178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17647711	0.85[EUR][1000 genomes]
rs17848068	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1856791	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1908089	0.88[CEU][hapmap]
rs2029682	0.88[CEU][hapmap]
rs2147039	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4403585	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4638068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646960	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57249318	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5745325	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs5745331	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs5745347	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs5745383	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs5745394	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs5745430	0.87[CEU][hapmap]
rs60550898	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6656501	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6664254	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6675212	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6704444	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs721204	1.00[CHB][hapmap]
rs74090722	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74090730	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[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	nsv945914	chr1:76109781-76172388	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1846233	RABGGTB	cis	cerebellum	SCAN
rs1846233	SNORD45B	cis	parietal	SCAN
rs1846233	PIGK	cis	parietal	SCAN
rs1846233	SNORD45B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76159200-76159800	Flanking Active TSS	K562	blood

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