Variant report

Variant	rs12280107
Chromosome Location	chr11:59025022-59025023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59022960..59025371-chr11:59027303..59028814,2	K562	blood:
2	chr11:59020470..59022310-chr11:59023811..59025321,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1048444	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10792228	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10896953	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10896956	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896958	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11229896	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229898	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229899	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11600294	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17153461	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1938593	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1945592	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1945593	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2000875	0.89[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3847	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4938915	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4939260	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4939263	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4939267	0.96[CEU][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4939269	0.80[MEX][hapmap]
rs5023474	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5023475	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61689139	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6591510	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6591515	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6591517	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7109866	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7111287	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7113607	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7121247	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7129035	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7129362	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7931234	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7938115	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3381199	chr11:59015574-59068938	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12280107	CYBASC3	cis	parietal	SCAN
rs12280107	CYBASC3	cis	cerebellum	SCAN
rs12280107	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs12280107	MPEG1	cis	lymphoblastoid	seeQTL
rs12280107	UBE2L6	cis	parietal	SCAN
rs12280107	SNORD28	cis	cerebellum	SCAN
rs12280107	MPEG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59022800-59025400	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr11:59023000-59026600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr11:59024000-59028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:59024200-59030800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:59024200-59030800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:59025000-59025200	Enhancers	Lung	lung
7	chr11:59025000-59027200	Weak transcription	Primary monocytes fromperipheralblood	blood

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