Variant report

Variant	rs975409
Chromosome Location	chr20:1498614-1498615
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1495247..1497047-chr20:1498389..1500531,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1121670	1.00[ASN][1000 genomes]
rs1121671	1.00[ASN][1000 genomes]
rs1121672	1.00[ASN][1000 genomes]
rs2246154	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2249317	1.00[CEU][hapmap];0.83[MEX][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2249549	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2249962	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2250199	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2250289	0.84[AMR][1000 genomes]
rs2251801	0.98[ASN][1000 genomes]
rs2251811	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2252155	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2256520	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2262338	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2263655	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2263657	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2263658	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2422576	0.94[ASN][1000 genomes]
rs2422577	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2422578	0.94[ASN][1000 genomes]
rs2422579	0.94[ASN][1000 genomes]
rs2422580	0.93[ASN][1000 genomes]
rs2422582	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422584	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422585	1.00[ASN][1000 genomes]
rs2422586	1.00[ASN][1000 genomes]
rs2422587	1.00[ASN][1000 genomes]
rs2422588	1.00[ASN][1000 genomes]
rs2422592	0.89[ASN][1000 genomes]
rs2422593	1.00[ASN][1000 genomes]
rs2422594	1.00[ASN][1000 genomes]
rs2422595	1.00[ASN][1000 genomes]
rs2422597	0.99[ASN][1000 genomes]
rs2422599	0.99[ASN][1000 genomes]
rs2422600	0.99[ASN][1000 genomes]
rs2422601	0.99[ASN][1000 genomes]
rs2422602	0.99[ASN][1000 genomes]
rs2422603	0.99[ASN][1000 genomes]
rs2422604	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2422605	0.99[ASN][1000 genomes]
rs2422606	0.98[ASN][1000 genomes]
rs2422607	0.98[ASN][1000 genomes]
rs2422608	0.98[ASN][1000 genomes]
rs2422610	0.98[ASN][1000 genomes]
rs2422611	0.98[ASN][1000 genomes]
rs2422612	0.85[AMR][1000 genomes]
rs3761269	0.88[CEU][hapmap]
rs3848784	0.93[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes]
rs4476414	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813157	1.00[ASN][1000 genomes]
rs4813158	1.00[ASN][1000 genomes]
rs6034006	0.88[CEU][hapmap];0.90[AMR][1000 genomes]
rs6042710	0.94[ASN][1000 genomes]
rs6042711	0.93[ASN][1000 genomes]
rs6135158	0.99[ASN][1000 genomes]
rs761450	0.94[ASN][1000 genomes]
rs761451	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs975409	C20orf141	cis	parietal	SCAN
rs975409	SIRPB1	cis	Whole Blood	GTEx
rs975409	RP4-576H24.5	cis	Whole Blood	GTEx
rs975409	SIRPB1	cis	Nerve Tibial	GTEx
rs975409	SIRPB1	cis	multi-tissue	Pritchard
rs975409	RSPO4	cis	parietal	SCAN
rs975409	DEFB126	cis	parietal	SCAN
rs975409	SIRPB1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1497600-1499400	Enhancers	H9 Cell Line	embryonic stem cell
2	chr20:1497800-1498800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr20:1498000-1499400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:1498200-1498800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr20:1498400-1499200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr20:1498400-1499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:1498600-1499000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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