Variant report

Variant	rs678208
Chromosome Location	chr12:10142538-10142539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1060648	0.83[GIH][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs1081386	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273986	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2961544	0.83[GIH][hapmap];1.00[YRI][hapmap]
rs4611291	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4764177	0.83[GIH][hapmap]
rs476844	0.84[ASN][1000 genomes]
rs479499	0.84[ASN][1000 genomes]
rs519291	0.81[AFR][1000 genomes]
rs531425	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs544783	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566229	0.81[AFR][1000 genomes]
rs570082	0.81[AFR][1000 genomes]
rs574097	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs576031	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs588272	0.83[GIH][hapmap];0.84[ASN][1000 genomes]
rs608418	0.83[AFR][1000 genomes]
rs613871	0.83[MEX][hapmap]
rs623269	0.83[AFR][1000 genomes]
rs623728	0.83[AFR][1000 genomes]
rs632963	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs633874	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs636554	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679982	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684134	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1038226	chr12:10121288-10143591	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv525593	chr12:10121347-10156646	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv898756	chr12:10142538-10174314	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs678208	RP11-133L14.5	cis	Whole Blood	GTEx
rs678208	LOC653113	cis	parietal	SCAN
rs678208	RPL13AP20	cis	cerebellum	SCAN
rs678208	UNQ5782	cis	multi-tissue	Pritchard
rs678208	TAS2R13	cis	parietal	SCAN
rs678208	CLEC12A	cis	multi-tissue	Pritchard
rs678208	CLEC12A	cis	Whole Blood	GTEx
rs678208	CLEC12A	cis	Artery Tibial	GTEx
rs678208	CLEC12B	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10129200-10144400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:10135800-10144600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:10138800-10142600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:10139400-10143400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:10140200-10143400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:10140800-10144400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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