Variant report

Variant	rs2422609
Chromosome Location	chr20:1503297-1503298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2224878	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2249431	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2249832	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2250055	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2250091	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2252400	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252401	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252425	0.92[ASN][1000 genomes]
rs2253429	1.00[JPT][hapmap]
rs2253693	1.00[JPT][hapmap]
rs2253698	1.00[JPT][hapmap]
rs2253815	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2253821	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2255641	0.92[ASN][1000 genomes]
rs2255651	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2255988	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2256095	1.00[JPT][hapmap]
rs2256229	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2256240	1.00[JPT][hapmap]
rs2256243	1.00[JPT][hapmap]
rs2256250	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2256251	1.00[JPT][hapmap]
rs2263654	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2263656	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2263660	0.92[ASN][1000 genomes]
rs2263663	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2422613	1.00[JPT][hapmap]
rs2422614	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2422618	0.92[ASN][1000 genomes]
rs6074896	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7264491	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2422609	SIRPD	cis	Whole Blood	GTEx
rs2422609	TMC2	cis	parietal	SCAN
rs2422609	C20orf141	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1500800-1504800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr20:1501600-1503400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr20:1502000-1503600	Weak transcription	Dnd41	blood
4	chr20:1502400-1505800	Weak transcription	Spleen	Spleen
5	chr20:1502600-1503600	Weak transcription	Primary hematopoietic stem cells	blood

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