Variant report

Variant	rs616408
Chromosome Location	chr1:212716033-212716034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:212715993-212716328	GM12878	blood:	n/a	chr1:212716134-212716145

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212715838..212717810-chr1:212781601..212784590,2	K562	blood:
2	chr1:212715838..212718756-chr1:212781123..212784590,3	K562	blood:

Variant related genes	Relation type
ENSG00000228067	TF binding region
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10779581	0.85[JPT][hapmap]
rs10863978	0.85[JPT][hapmap]
rs10863980	0.81[JPT][hapmap]
rs11119957	0.85[JPT][hapmap]
rs11119963	0.81[ASN][1000 genomes]
rs11119964	0.84[GIH][hapmap]
rs11119965	0.83[ASN][1000 genomes]
rs11119967	0.84[GIH][hapmap]
rs11119971	0.80[CHD][hapmap];0.92[JPT][hapmap]
rs11805307	0.82[YRI][hapmap]
rs1877474	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4951453	0.82[ASN][1000 genomes]
rs4951609	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4951611	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs502502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510189	0.81[ASN][1000 genomes]
rs587293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606996	0.82[ASN][1000 genomes]
rs678640	0.82[ASN][1000 genomes]
rs791561	0.82[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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
7	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs616408	LAMB3	cis	cerebellum	SCAN
rs616408	C1orf107	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212714000-212722600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212714200-212719000	Weak transcription	Brain Anterior Caudate	brain
3	chr1:212714200-212719000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:212714200-212719200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:212714400-212719200	Weak transcription	Brain Substantia Nigra	brain
6	chr1:212714600-212719000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:212715200-212717800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:212715400-212716400	Enhancers	GM12878-XiMat	blood
9	chr1:212715400-212716600	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:212715400-212717000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:212715800-212718600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:212716000-212716200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:212716000-212716200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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