Variant report

Variant	rs7109716
Chromosome Location	chr11:74776211-74776212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74775284..74777125-chr11:74778388..74781145,2	K562	blood:
2	chr11:74775844..74777522-chr11:74789368..74791115,2	K562	blood:
3	chr11:74775986..74778736-chr11:74786345..74788649,2	K562	blood:
4	chr11:74764412..74766619-chr11:74774749..74776362,2	MCF-7	breast:
5	chr11:74773998..74776628-chr11:74806307..74808054,2	K562	blood:
6	chr11:74772361..74774427-chr11:74774616..74776750,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10793112	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899053	0.89[YRI][hapmap]
rs10899059	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10899060	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10899061	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899064	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899065	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11236289	0.83[AFR][1000 genomes]
rs11236294	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11236296	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11236303	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236304	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236306	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236307	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236309	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236310	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236311	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236313	0.95[EUR][1000 genomes]
rs11600328	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223822	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12226763	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12577127	0.81[GIH][hapmap]
rs1371410	0.81[GIH][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4245440	0.81[GIH][hapmap]
rs4387374	0.81[GIH][hapmap]
rs4456280	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4531492	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4554917	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944970	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944971	0.86[AMR][1000 genomes]
rs56885894	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7106757	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7396866	0.81[GIH][hapmap]
rs7482760	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7483351	0.90[YRI][hapmap];0.83[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897918	chr11:74757641-74798928	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs7109716	RNF169	cis	lymphoblastoid	seeQTL
rs7109716	XRRA1	cis	Thyroid	GTEx
rs7109716	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs7109716	XRRA1	cis	normal skin	skin_eQTL
rs7109716	XRRA1	cis	lymphoblastoid	GTEx
rs7109716	XRRA1	cis	Nerve Tibial	GTEx
rs7109716	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs7109716	XRRA1	cis	lung	GTEx
rs7109716	XRRA1	cis	Whole Blood	GTEx
rs7109716	XRRA1	cis	lymphoblastoid	seeQTL
rs7109716	XRRA1	cis	Esophagus Mucosa	GTEx
rs7109716	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs7109716	RP11-147I3.1	cis	Thyroid	GTEx
rs7109716	XRRA1	cis	Esophagus Muscularis	GTEx
rs7109716	XRRA1	cis	Stomach	GTEx
rs7109716	XRRA1	cis	Muscle Skeletal	GTEx
rs7109716	XRRA1	cis	Heart Left Ventricle	GTEx
rs7109716	XRRA1	cis	Artery Tibial	GTEx
rs7109716	XRRA1	cis	Adipose Subcutaneous	GTEx
rs7109716	XRRA1	cis	Artery Aorta	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74773800-74782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74775200-74777000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:74775400-74776600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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