Variant report

Variant	rs11575535
Chromosome Location	chr7:50531994-50531995
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	chr7:50515983..50518420-chr7:50531450..50533069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132436	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10499693	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575302	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11575340	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11575494	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11575501	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575502	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575504	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575507	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575508	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575510	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575511	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575512	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575514	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575518	0.90[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575519	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575522	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575523	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575527	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575537	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11575540	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575542	0.81[ASW][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575543	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575546	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575547	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575549	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11978797	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11981575	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11982708	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11982772	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11982776	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11983581	0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11983757	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17133877	1.00[CEU][hapmap]
rs6975312	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs73695681	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73695682	0.90[AMR][1000 genomes]
rs73695683	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73695684	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs930707	1.00[GIH][hapmap];1.00[TSI][hapmap]

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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1026081	chr7:50525900-50538184	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11575535	PGAM2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50518800-50535400	Weak transcription	Pancreas	Pancrea
2	chr7:50518800-50535600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:50518800-50535600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:50518800-50535600	Weak transcription	HepG2	liver
5	chr7:50528800-50533800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr7:50528800-50535400	Weak transcription	Colonic Mucosa	Colon
7	chr7:50529200-50535600	Strong transcription	Fetal Intestine Large	intestine
8	chr7:50529600-50535400	Strong transcription	Fetal Intestine Small	intestine
9	chr7:50530000-50533200	Strong transcription	Liver	Liver
10	chr7:50530400-50533600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:50530400-50535400	Weak transcription	HUVEC	blood vessel
12	chr7:50531000-50535400	Weak transcription	Hela-S3	cervix
13	chr7:50531800-50532200	Weak transcription	Rectal Mucosa Donor 29	rectum

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