Variant report

Variant	rs3990027
Chromosome Location	chr11:102359665-102359666
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102354515..102357705-chr11:102357749..102361369,4	K562	blood:
2	chr11:102358831..102361253-chr11:102363171..102365874,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10750642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791576	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186992	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850437	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs4754045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs488324	1.00[ASN][1000 genomes]
rs514188	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs555650	0.96[ASN][1000 genomes]
rs562383	0.99[ASN][1000 genomes]
rs599384	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs603608	0.96[ASN][1000 genomes]
rs634743	0.99[ASN][1000 genomes]
rs634814	1.00[ASN][1000 genomes]
rs636898	0.99[ASN][1000 genomes]
rs650423	0.99[ASN][1000 genomes]
rs651319	0.99[ASN][1000 genomes]
rs653586	0.92[ASN][1000 genomes]
rs6590964	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6590966	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6590967	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs659789	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs665124	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs668660	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs938598	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938600	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv469990	chr11:102335609-102413943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv556150	chr11:102335609-102415859	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv468854	chr11:102336617-102413943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv556151	chr11:102336617-102413943	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3990027	TMEM123	Cis_1M	lymphoblastoid	RTeQTL
rs3990027	PDGFD	cis	parietal	SCAN
rs3990027	TMEM123	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102353400-102361400	Enhancers	HepG2	liver
2	chr11:102358400-102360000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:102358400-102360000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:102358400-102364200	Weak transcription	Fetal Intestine Small	intestine
5	chr11:102358400-102365600	Weak transcription	Primary T cells from cord blood	blood
6	chr11:102358600-102360000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:102358600-102360800	Enhancers	GM12878-XiMat	blood
8	chr11:102359200-102359800	Enhancers	Esophagus	oesophagus
9	chr11:102359200-102360400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:102359600-102359800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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