Variant report

Variant	rs9467231
Chromosome Location	chr6:24559587-24559588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24493986..24495664-chr6:24558273..24561120,2	MCF-7	breast:
2	chr6:24521872..24523462-chr6:24559517..24561128,2	K562	blood:

Variant related genes	Relation type
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs16889440	0.92[CHB][hapmap]
rs2076313	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2243831	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251350	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267539	0.92[CHB][hapmap]
rs2744540	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744541	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744542	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744543	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744544	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2744557	1.00[JPT][hapmap]
rs2744607	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744608	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744609	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760159	1.00[JPT][hapmap]
rs2760165	1.00[CHB][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs2760166	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760167	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760168	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2760172	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760173	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760174	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760175	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2760179	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2817198	1.00[JPT][hapmap]
rs2817245	0.92[CHB][hapmap]
rs2817249	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817250	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817251	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817252	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817253	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817254	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817255	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857543	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3896132	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456617	0.82[CHB][hapmap]
rs9467220	1.00[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1020653	chr6:24557870-24638244	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9467231	PGBD1	cis	parietal	SCAN
rs9467231	MRS2	cis	cerebellum	SCAN
rs9467231	MRS2L	cis	multi-tissue	Pritchard
rs9467231	BTN3A1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
2	chr6:24535200-24566600	Weak transcription	Brain Germinal Matrix	brain
3	chr6:24535200-24591200	Weak transcription	Fetal Brain Male	brain
4	chr6:24535600-24560600	Weak transcription	Brain Anterior Caudate	brain
5	chr6:24535600-24560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:24535600-24563200	Weak transcription	Brain Angular Gyrus	brain
7	chr6:24535600-24583400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:24539200-24583200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:24548400-24583400	Weak transcription	A549	lung
10	chr6:24550200-24566400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:24552600-24568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:24554600-24563600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:24559200-24559600	Enhancers	Pancreas	Pancrea
14	chr6:24559200-24559800	Strong transcription	Fetal Brain Female	brain

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