Variant report

Variant	rs4245439
Chromosome Location	chr11:74732230-74732231
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74725568..74728361-chr11:74730920..74733863,2	MCF-7	breast:
2	chr11:74731114..74733845-chr11:74735387..74737744,2	K562	blood:
3	chr11:74659749..74661462-chr11:74730590..74733403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166435	Chromatin interaction
ENSG00000118363	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10793111	0.80[ASN][1000 genomes]
rs10899066	0.80[ASN][1000 genomes]
rs11530865	0.80[ASN][1000 genomes]
rs11605604	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs12363224	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs1282460	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs1282692	0.84[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs1292895	0.84[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs1297319	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs1583342	0.84[CEU][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs2033532	0.84[CEU][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs2851136	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2919057	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4335576	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs4373962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592443	0.80[ASN][1000 genomes]
rs473256	0.84[CEU][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs480840	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs488115	0.86[CHD][hapmap];0.82[MEX][hapmap]
rs4944067	0.86[CHD][hapmap]
rs511890	0.84[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs512780	0.82[JPT][hapmap]
rs519741	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs527529	0.88[JPT][hapmap]
rs529488	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs537054	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs538502	0.88[JPT][hapmap]
rs543244	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs550980	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs567956	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs568558	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs568758	0.81[CEU][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap]
rs577063	0.81[ASN][1000 genomes]
rs590105	0.81[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs594144	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599722	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs603062	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs614832	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs624786	0.84[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs625268	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs641584	0.83[CEU][hapmap];0.87[JPT][hapmap];0.91[TSI][hapmap]
rs643807	0.83[CHD][hapmap];0.88[JPT][hapmap]
rs646287	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs688665	0.81[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs7110411	0.80[ASN][1000 genomes]
rs7937160	0.80[ASN][1000 genomes]
rs7938876	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444	0.84[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs997465	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4245439	XRRA1	cis	Esophagus Mucosa	GTEx
rs4245439	RP11-147I3.1	cis	Thyroid	GTEx
rs4245439	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs4245439	XRRA1	cis	lymphoblastoid	seeQTL
rs4245439	XRRA1	cis	lesional skin	skin_eQTL
rs4245439	XRRA1	cis	Adipose Subcutaneous	GTEx
rs4245439	XRRA1	cis	Nerve Tibial	GTEx
rs4245439	XRRA1	cis	Muscle Skeletal	GTEx
rs4245439	RNF169	cis	cerebellum	SCAN
rs4245439	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs4245439	XRRA1	cis	cerebellum	SCAN
rs4245439	XRRA1	cis	lung	GTEx
rs4245439	RNF169	cis	lymphoblastoid	seeQTL
rs4245439	XRRA1	cis	Whole Blood	GTEx
rs4245439	KRTAP5-10	cis	parietal	SCAN
rs4245439	XRRA1	cis	Thyroid	GTEx
rs4245439	XRRA1	cis	Artery Tibial	GTEx
rs4245439	XRRA1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74718000-74733800	Weak transcription	Brain Substantia Nigra	brain
2	chr11:74718000-74734200	Weak transcription	Right Ventricle	heart
3	chr11:74721600-74733400	Weak transcription	Pancreas	Pancrea
4	chr11:74721600-74734200	Weak transcription	Brain Angular Gyrus	brain
5	chr11:74721600-74734200	Weak transcription	Brain Anterior Caudate	brain
6	chr11:74721600-74734200	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:74721600-74734200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:74721600-74734200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:74723800-74733800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:74724000-74734200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:74724600-74735400	Weak transcription	Aorta	Aorta
12	chr11:74725600-74737000	Weak transcription	Thymus	Thymus
13	chr11:74726600-74746400	Weak transcription	GM12878-XiMat	blood
14	chr11:74729400-74732600	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr11:74730600-74734200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:74731000-74733400	Weak transcription	Fetal Intestine Large	intestine
17	chr11:74731600-74732800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:74731800-74732400	Enhancers	Fetal Muscle Trunk	muscle
19	chr11:74731800-74732400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr11:74731800-74732600	Enhancers	Left Ventricle	heart
21	chr11:74731800-74732800	Enhancers	Psoas Muscle	Psoas
22	chr11:74732000-74732600	Enhancers	Fetal Heart	heart
23	chr11:74732000-74733800	Weak transcription	Right Atrium	heart
24	chr11:74732000-74734800	Enhancers	Fetal Muscle Leg	muscle
25	chr11:74732000-74737800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr11:74732200-74733800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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