Variant report

Variant	rs4245440
Chromosome Location	chr11:74736534-74736535
allele	C/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	chr11:74735037..74738076-chr11:74739578..74743137,3	K562	blood:
3	chr11:74659558..74661060-chr11:74734935..74736828,2	K562	blood:
4	chr11:74731114..74733845-chr11:74735387..74737744,2	K562	blood:
5	chr11:74699633..74701295-chr11:74736217..74739161,2	K562	blood:
6	chr11:74734239..74737191-chr11:74823772..74825545,2	K562	blood:

Variant related genes	Relation type
ENSG00000166435	Chromatin interaction
ENSG00000162139	Chromatin interaction
ENSG00000118363	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10751241	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs10793107	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899052	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs10899053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899054	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899058	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]
rs10899059	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899060	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236281	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236289	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236290	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236296	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11603294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12221841	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs12577127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577614	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1371410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119028	0.96[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs2165162	0.96[CEU][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2165163	0.96[CEU][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2298746	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs2304683	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs3814726	0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs4387374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456280	0.90[GIH][hapmap]
rs4944960	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs4944961	0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs4944965	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944968	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56194145	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105085	0.91[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs7128739	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs725460	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7396866	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7483351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs919877	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs9787775	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9787897	0.80[ASN][1000 genomes]

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs4245440	XRRA1	cis	Thyroid	GTEx
rs4245440	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs4245440	XRRA1	cis	Artery Tibial	GTEx
rs4245440	PLEKHB1	cis	cerebellum	SCAN
rs4245440	XRRA1	cis	parietal	SCAN
rs4245440	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs4245440	XRRA1	cis	Muscle Skeletal	GTEx
rs4245440	XRRA1	cis	Stomach	GTEx
rs4245440	RP11-147I3.1	cis	Thyroid	GTEx
rs4245440	XRRA1	cis	lung	GTEx
rs4245440	XRRA1	cis	lymphoblastoid	GTEx
rs4245440	XRRA1	cis	Adipose Subcutaneous	GTEx
rs4245440	XRRA1	cis	Esophagus Mucosa	GTEx
rs4245440	XRRA1	cis	Heart Left Ventricle	GTEx
rs4245440	XRRA1	cis	Esophagus Muscularis	GTEx
rs4245440	XRRA1	cis	Whole Blood	GTEx
rs4245440	RNF169	cis	lymphoblastoid	seeQTL
rs4245440	XRRA1	cis	Nerve Tibial	GTEx
rs4245440	XRRA1	cis	lymphoblastoid	seeQTL
rs4245440	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs4245440	RNF169	cis	cerebellum	SCAN
rs4245440	XRRA1	cis	cerebellum	SCAN
rs4245440	XRRA1	cis	Artery Aorta	GTEx
rs4245440	PAAF1	cis	parietal	SCAN
rs4245440	XRRA1	cis	lesional skin	skin_eQTL
rs4245440	XRRA1	cis	normal skin	skin_eQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74725600-74737000	Weak transcription	Thymus	Thymus
2	chr11:74726600-74746400	Weak transcription	GM12878-XiMat	blood
3	chr11:74732000-74737800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr11:74732400-74736600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr11:74733200-74736800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr11:74733200-74738400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:74734200-74736600	Enhancers	Brain Anterior Caudate	brain
8	chr11:74734200-74736800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr11:74734400-74742200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:74734600-74739000	Weak transcription	Psoas Muscle	Psoas
11	chr11:74735000-74739200	Weak transcription	NHDF-Ad	bronchial
12	chr11:74735200-74741600	Weak transcription	Left Ventricle	heart
13	chr11:74735400-74738600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:74735400-74742400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:74736200-74736600	Genic enhancers	Fetal Intestine Small	intestine
16	chr11:74736400-74737400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:74736400-74737800	Weak transcription	K562	blood
18	chr11:74736400-74741800	Weak transcription	Brain Angular Gyrus	brain
19	chr11:74736400-74741800	Weak transcription	Brain Substantia Nigra	brain
20	chr11:74736400-74741800	Weak transcription	Fetal Intestine Large	intestine

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