Variant report

Variant	rs4240927
Chromosome Location	chr1:221958189-221958190
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	chr1:221950355..221953290-chr1:221957212..221959262,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10495177	0.84[ASN][1000 genomes]
rs11588738	0.85[ASN][1000 genomes]
rs12029988	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs3010839	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3010840	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34557512	0.92[ASN][1000 genomes]
rs35907150	0.80[ASN][1000 genomes]
rs4846723	0.80[ASN][1000 genomes]
rs4846724	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6604671	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9441956	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv873201	chr1:221956626-222007535	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4240927	C1orf58	cis	cerebellum	SCAN
rs4240927	USH2A	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221948800-221958200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:221949800-221958200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:221954000-221966400	Weak transcription	Spleen	Spleen
4	chr1:221955600-221958200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:221955600-221958400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:221955800-221958200	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:221956000-221958200	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:221956000-221958200	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:221956000-221958200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:221956200-221958200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:221956200-221958600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:221956200-221960000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:221957200-221958200	Enhancers	Thymus	Thymus
14	chr1:221957400-221958200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:221957400-221958200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:221957400-221958200	Enhancers	Brain Substantia Nigra	brain
17	chr1:221957400-221958200	Enhancers	Fetal Thymus	thymus
18	chr1:221957400-221958400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:221957400-221958400	Enhancers	Brain Anterior Caudate	brain
20	chr1:221957400-221958600	Enhancers	Primary T cells from cord blood	blood
21	chr1:221957400-221963000	Weak transcription	Adipose Nuclei	Adipose
22	chr1:221957600-221958200	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:221957600-221958200	Enhancers	Brain Germinal Matrix	brain
24	chr1:221957800-221958200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:221958000-221958400	Enhancers	Brain Angular Gyrus	brain
26	chr1:221958000-221960000	Enhancers	Dnd41	blood

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