Variant report

Variant	rs4845549
Chromosome Location	chr1:153472285-153472286
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	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
2	chr1:153466147..153468573-chr1:153470167..153472287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000163218	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs16835366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835368	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835393	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17695220	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1887039	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1964151	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339696	0.88[ASN][1000 genomes]
rs28410699	0.88[ASN][1000 genomes]
rs28464843	0.88[ASN][1000 genomes]
rs28632016	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28635377	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28676601	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28707433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2879553	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap]
rs3915524	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272569	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4430277	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4845351	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4845352	1.00[JPT][hapmap]
rs4845548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845551	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845552	0.81[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845553	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845554	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6587743	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6587745	0.88[ASN][1000 genomes]
rs6587746	0.88[ASN][1000 genomes]
rs6660055	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6672390	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6679509	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6684970	0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs6690638	0.85[ASN][1000 genomes]
rs6690712	0.85[ASN][1000 genomes]
rs6696893	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515940	0.85[ASN][1000 genomes]
rs7518306	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7520093	0.88[ASN][1000 genomes]
rs7534343	0.86[ASN][1000 genomes]
rs7534347	0.88[ASN][1000 genomes]
rs7534830	0.85[ASN][1000 genomes]
rs7537898	0.85[ASN][1000 genomes]
rs7544359	0.85[ASN][1000 genomes]
rs9436094	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9436095	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4845549	PSMB4	cis	parietal	SCAN
rs4845549	GBA	cis	parietal	SCAN
rs4845549	LCE2C	cis	parietal	SCAN
rs4845549	PSMD4	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153462800-153479000	Weak transcription	Right Atrium	heart
2	chr1:153467200-153478000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:153468400-153479000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:153471200-153472400	Enhancers	Aorta	Aorta
5	chr1:153471200-153472400	Enhancers	Fetal Lung	lung
6	chr1:153471800-153477800	Weak transcription	Ovary	ovary
7	chr1:153471800-153478800	Weak transcription	Fetal Stomach	stomach

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