Variant report

Variant	rs6034006
Chromosome Location	chr20:1519511-1519512
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:59)

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];0.82[JPT][hapmap]
rs12480515	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1535882	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2209313	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap]
rs2243423	0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2243425	0.82[ASN][1000 genomes]
rs2243529	0.82[ASN][1000 genomes]
rs2243602	0.87[ASN][1000 genomes]
rs2243603	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs2246154	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]
rs2249317	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249549	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249962	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2250199	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2250289	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2251811	0.81[AMR][1000 genomes]
rs2252155	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2253427	0.93[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap]
rs2253814	0.89[ASN][1000 genomes]
rs2254194	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2254448	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2254458	0.85[ASN][1000 genomes]
rs2256520	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2262338	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2263655	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2263657	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263658	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263664	0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs2317870	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs2422577	0.87[AMR][1000 genomes]
rs2422582	0.87[AMR][1000 genomes]
rs2422584	0.90[AMR][1000 genomes]
rs2422604	0.90[AMR][1000 genomes]
rs2422612	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2422615	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2422631	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs2746609	0.93[CHB][hapmap]
rs2873569	0.83[LWK][hapmap]
rs3761268	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs3761269	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3848783	0.86[ASN][1000 genomes]
rs3848784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3848785	0.86[ASN][1000 genomes]
rs3848786	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3848787	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3848788	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4476414	0.85[AMR][1000 genomes]
rs6034039	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6042909	0.86[ASN][1000 genomes]
rs6079527	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6079531	0.88[ASN][1000 genomes]
rs6105334	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6110353	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs6514526	0.86[ASN][1000 genomes]
rs761451	0.87[AMR][1000 genomes]
rs975409	0.90[AMR][1000 genomes]
rs975410	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
9	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
10	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
11	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6034006	RP4-576H24.5	cis	Whole Blood	GTEx
rs6034006	SIRPB1	cis	Nerve Tibial	GTEx
rs6034006	SIRPB1	cis	lung	GTEx
rs6034006	RSPO4	cis	cerebellum	SCAN
rs6034006	SIRPB1	cis	Whole Blood	GTEx
rs6034006	SIRPB1	cis	Adipose Subcutaneous	GTEx
rs6034006	SIRPB1	cis	multi-tissue	Pritchard
rs6034006	C6orf226	trans	parietal	SCAN
rs6034006	DEFB126	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1516000-1519600	Enhancers	Primary B cells from peripheral blood	blood
2	chr20:1518400-1520400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr20:1518600-1519800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr20:1518600-1519800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:1518600-1519800	Enhancers	HMEC	breast
6	chr20:1518800-1519600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr20:1518800-1519800	Enhancers	Primary B cells from cord blood	blood
8	chr20:1519000-1519600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:1519000-1520400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:1519000-1520400	Enhancers	NHEK	skin
11	chr20:1519400-1520400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr20:1519400-1520600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr20:1519400-1521800	Weak transcription	Primary hematopoietic stem cells	blood

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