Variant report

Variant	rs10899058
Chromosome Location	chr11:74738814-74738815
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74732707..74737520-chr11:74738671..74743586,5	MCF-7	breast:
2	chr11:74721191..74723681-chr11:74738693..74740282,2	K562	blood:
3	chr11:74699633..74701295-chr11:74736217..74739161,2	K562	blood:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10751241	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs10793107	0.95[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899052	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs10899053	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899054	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899059	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899060	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236281	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236282	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236289	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236290	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236296	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11603294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221841	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs12577127	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12577614	0.83[AMR][1000 genomes]
rs1371410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119028	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs2165162	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs2165163	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs2298746	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs2304683	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs3814726	0.95[JPT][hapmap]
rs4245440	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4387374	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944960	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs4944961	0.95[JPT][hapmap]
rs4944965	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944968	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56194145	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7105085	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs7128739	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs725460	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7396866	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7483351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919877	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs9787775	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes]

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs10899058	XRRA1	cis	Esophagus Mucosa	GTEx
rs10899058	RP11-147I3.1	cis	Thyroid	GTEx
rs10899058	XRRA1	cis	Heart Left Ventricle	GTEx
rs10899058	XRRA1	cis	lesional skin	skin_eQTL
rs10899058	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs10899058	XRRA1	cis	Artery Tibial	GTEx
rs10899058	XRRA1	cis	Thyroid	GTEx
rs10899058	XRRA1	cis	Esophagus Muscularis	GTEx
rs10899058	XRRA1	cis	Stomach	GTEx
rs10899058	XRRA1	cis	normal skin	skin_eQTL
rs10899058	XRRA1	cis	Whole Blood	GTEx
rs10899058	XRRA1	cis	Nerve Tibial	GTEx
rs10899058	XRRA1	cis	Adipose Subcutaneous	GTEx
rs10899058	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs10899058	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs10899058	XRRA1	cis	Muscle Skeletal	GTEx
rs10899058	XRRA1	cis	lung	GTEx
rs10899058	XRRA1	cis	Artery Aorta	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74726600-74746400	Weak transcription	GM12878-XiMat	blood
2	chr11:74734400-74742200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:74734600-74739000	Weak transcription	Psoas Muscle	Psoas
4	chr11:74735000-74739200	Weak transcription	NHDF-Ad	bronchial
5	chr11:74735200-74741600	Weak transcription	Left Ventricle	heart
6	chr11:74735400-74742400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:74736400-74741800	Weak transcription	Brain Angular Gyrus	brain
8	chr11:74736400-74741800	Weak transcription	Brain Substantia Nigra	brain
9	chr11:74736400-74741800	Weak transcription	Fetal Intestine Large	intestine
10	chr11:74736600-74742200	Weak transcription	Fetal Intestine Small	intestine
11	chr11:74737800-74739800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:74737800-74741600	Enhancers	K562	blood
13	chr11:74738200-74743200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:74738400-74739600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:74738600-74739000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:74738600-74743200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:74738800-74740000	Enhancers	Skeletal Muscle Male	skeletal muscle

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