Variant report

Variant	rs2246154
Chromosome Location	chr20:1528038-1528039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11696739	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11696842	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs11697985	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs12480515	0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1535882	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2209313	0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs2243423	0.93[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2243425	0.84[ASN][1000 genomes]
rs2243529	0.84[ASN][1000 genomes]
rs2243602	0.89[ASN][1000 genomes]
rs2243603	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2249317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249962	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250289	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2251811	0.86[AMR][1000 genomes]
rs2252155	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2253427	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2253814	0.91[ASN][1000 genomes]
rs2254194	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2254448	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs2254458	0.87[ASN][1000 genomes]
rs2256520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2262338	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2263655	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2263657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2263658	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2263664	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2317870	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs2422577	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2422582	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2422584	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2422604	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2422612	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2422615	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2422631	0.93[CHB][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs2746608	0.85[YRI][hapmap]
rs2746609	0.93[CHB][hapmap]
rs2873569	1.00[YRI][hapmap]
rs3761268	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs3761269	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3848783	0.88[ASN][1000 genomes]
rs3848784	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848785	0.88[ASN][1000 genomes]
rs3848786	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3848787	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3848788	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4476414	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6034006	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6034039	0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6042909	0.88[ASN][1000 genomes]
rs6079527	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6079531	0.86[ASN][1000 genomes]
rs6105334	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6110353	0.93[CHB][hapmap]
rs6514526	0.84[ASN][1000 genomes]
rs761451	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs975409	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs975410	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	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
5	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
6	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
7	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
8	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv510779	chr20:1509330-1613962	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2246154	SIRPB1	cis	lung	GTEx
rs2246154	SIRPB1	cis	Whole Blood	GTEx
rs2246154	RP4-576H24.5	cis	Whole Blood	GTEx
rs2246154	SIRPD	cis	Whole Blood	GTEx
rs2246154	SIRPB1	cis	Nerve Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1520600-1529800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr20:1527400-1529800	Weak transcription	Monocytes-CD14+_RO01746	blood

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