Variant report

Variant	rs4405907
Chromosome Location	chr3:118669017-118669018
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118654131..118656982-chr3:118667151..118670304,3	K562	blood:
2	chr3:118655482..118657417-chr3:118667049..118669730,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1016284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11709968	0.92[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715148	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11922973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12053925	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1435653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16829222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17738897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1836689	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1836691	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879553	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2160050	0.89[ASN][1000 genomes]
rs4687832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687834	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4687960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55742142	0.90[ASN][1000 genomes]
rs56232409	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56234333	0.90[ASN][1000 genomes]
rs60755482	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4405907	UPK1B	cis	frontal cortex	BrainEAC

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118662000-118679800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:118662000-118679800	Weak transcription	Ovary	ovary
3	chr3:118662800-118672000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:118662800-118672400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:118664400-118676400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:118666200-118677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:118666400-118669800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr3:118666600-118669200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:118666600-118669800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr3:118666600-118670200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:118666800-118669200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:118666800-118669400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:118666800-118669400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr3:118668000-118669800	Enhancers	Brain Substantia Nigra	brain
15	chr3:118668000-118670000	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:118668200-118669200	Enhancers	Brain Angular Gyrus	brain
17	chr3:118668200-118670000	Enhancers	Brain Anterior Caudate	brain
18	chr3:118668400-118670600	Enhancers	Primary T cells from cord blood	blood
19	chr3:118668600-118670200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr3:118668800-118670200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:118668800-118673000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:118668800-118674200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:118669000-118669400	Weak transcription	Fetal Heart	heart
24	chr3:118669000-118670000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:118669000-118673000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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