Variant report

Variant	rs8177177
Chromosome Location	chr3:133463195-133463196
allele	C/T
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	MAX	chr3:133463162-133463279	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133460249..133463891-chr3:133464263..133466995,3	MCF-7	breast:

Variant related genes	Relation type
TF	TF binding region
ENSG00000091513	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10433417	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10935073	0.80[ASN][1000 genomes]
rs11921527	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12493887	0.97[ASN][1000 genomes]
rs12639304	0.97[ASN][1000 genomes]
rs4241357	0.84[CEU][hapmap]
rs4355280	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4459901	0.91[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4481157	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4525863	0.80[ASN][1000 genomes]
rs6439431	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6439435	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6774822	0.94[ASN][1000 genomes]
rs6775042	0.97[ASN][1000 genomes]
rs6777860	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6780650	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6782523	0.80[ASN][1000 genomes]
rs6787177	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6790668	0.91[ASN][1000 genomes]
rs6798547	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7646118	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8177178	0.92[CEU][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8177197	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs8177224	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs9829019	0.98[ASN][1000 genomes]
rs9830001	0.80[CEU][hapmap]
rs9831392	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9869257	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9869535	0.90[AFR][1000 genomes];1.00[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8177177	PCCB	cis	cerebellum	SCAN
rs8177177	TOPBP1	cis	parietal	SCAN
rs8177177	SRPRB	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133460400-133464600	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr3:133460800-133464600	Enhancers	Brain Angular Gyrus	brain
3	chr3:133461600-133464400	Enhancers	Brain Cingulate Gyrus	brain
4	chr3:133461600-133464400	Enhancers	Brain Substantia Nigra	brain
5	chr3:133461800-133463400	Flanking Active TSS	HepG2	liver
6	chr3:133461800-133464400	Enhancers	Brain Hippocampus Middle	brain
7	chr3:133461800-133464600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:133462000-133464600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:133462200-133463600	Weak transcription	K562	blood
10	chr3:133462200-133464400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:133462200-133464400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:133462400-133464400	Enhancers	Brain Anterior Caudate	brain
13	chr3:133462600-133463400	Enhancers	Liver	Liver
14	chr3:133462800-133463600	Enhancers	Spleen	Spleen
15	chr3:133462800-133464400	Weak transcription	Pancreas	Pancrea

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