Variant report

Variant	rs608418
Chromosome Location	chr12:10131865-10131866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10130117..10132193-chr12:10133965..10136781,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC12B-1	chr12:10131565-10132123	NONHSAT026857
2	lnc-CLEC12B-1	chr12:10131565-10132123	NONHSAT026858

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1060648	0.88[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1081386	0.80[AFR][1000 genomes]
rs2961544	0.88[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs476844	0.87[AFR][1000 genomes]
rs479499	0.83[AFR][1000 genomes]
rs486134	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs519291	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531425	0.86[YRI][hapmap]
rs544783	0.81[AFR][1000 genomes]
rs566229	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570082	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592206	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs609216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623182	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs623269	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623728	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650368	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678208	0.83[AFR][1000 genomes]
rs679982	0.82[AFR][1000 genomes]
rs684134	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs608418	CLEC12A	cis	multi-tissue	Pritchard
rs608418	VAMP1	cis	cerebellum	SCAN
rs608418	LOC653113	cis	parietal	SCAN
rs608418	CLEC12A	cis	Thyroid	GTEx
rs608418	SCARNA12	cis	cerebellum	SCAN
rs608418	CLEC12B	cis	Whole Blood	GTEx
rs608418	RP11-133L14.5	cis	Whole Blood	GTEx
rs608418	CLEC12A	cis	Whole Blood	GTEx
rs608418	C12orf57	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10128000-10132600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
2	chr12:10129200-10144400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:10130400-10138600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:10130800-10132400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:10131200-10133600	Genic enhancers	Primary monocytes fromperipheralblood	blood

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