Variant report

Variant	rs538502
Chromosome Location	chr11:74560317-74560318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74552536..74554674-chr11:74560171..74562245,2	K562	blood:
2	chr11:74559768..74561678-chr11:74563525..74565103,2	K562	blood:
3	chr11:74547278..74549879-chr11:74556905..74560343,3	K562	blood:
4	chr11:74547278..74549231-chr11:74557755..74560343,2	K562	blood:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11236269	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11605604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12363224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1282460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282461	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1282689	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282690	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1282692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1282695	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1292895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1297319	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1303525	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1583342	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2033532	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2919057	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs41531051	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4245439	0.88[JPT][hapmap]
rs471462	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs473080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs473256	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs480840	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs483615	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4944945	0.91[YRI][hapmap]
rs495246	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs497772	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs502225	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505688	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs508319	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs511890	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs512780	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs519741	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs527529	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs529249	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs529488	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs537054	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs543244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs546643	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs550980	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs557483	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs561589	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs562265	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565767	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs567956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568558	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs568758	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs571446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs573925	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs577063	0.86[EUR][1000 genomes]
rs577102	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs580142	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs590105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs599722	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs603062	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs614832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs616085	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs624786	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs625268	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs629573	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs643807	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs646287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs688665	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997465	0.86[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
2	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs538502	XRRA1	cis	Adipose Subcutaneous	GTEx
rs538502	XRRA1	cis	Whole Blood	GTEx
rs538502	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs538502	XRRA1	cis	Muscle Skeletal	GTEx
rs538502	XRRA1	cis	Artery Tibial	GTEx
rs538502	XRRA1	cis	Esophagus Mucosa	GTEx
rs538502	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs538502	RP11-147I3.1	cis	Thyroid	GTEx
rs538502	XRRA1	cis	Thyroid	GTEx
rs538502	XRRA1	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:74545600-74564600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:74545600-74568400	Strong transcription	Fetal Intestine Large	intestine
6	chr11:74545800-74560400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:74545800-74565000	Strong transcription	Fetal Muscle Leg	muscle
8	chr11:74546000-74566800	Strong transcription	Fetal Stomach	stomach
9	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
10	chr11:74547800-74562800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:74548000-74560600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:74549400-74567600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:74549800-74560400	Weak transcription	Right Atrium	heart
14	chr11:74550600-74564600	Strong transcription	Fetal Intestine Small	intestine
15	chr11:74551000-74568400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:74552600-74560600	Strong transcription	Brain Cingulate Gyrus	brain
17	chr11:74552600-74565400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr11:74553800-74569400	Weak transcription	Fetal Heart	heart
20	chr11:74554200-74560400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr11:74554200-74567600	Weak transcription	Psoas Muscle	Psoas
22	chr11:74554600-74560800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:74554800-74571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:74555800-74560800	Weak transcription	HSMMtube	muscle
25	chr11:74555800-74569800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:74556200-74560600	Weak transcription	Brain Substantia Nigra	brain
27	chr11:74556200-74560800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr11:74556200-74561600	Weak transcription	GM12878-XiMat	blood
29	chr11:74556800-74562000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:74556800-74562400	Weak transcription	Hela-S3	cervix
31	chr11:74557200-74560600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:74557200-74561800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:74557200-74562800	Weak transcription	K562	blood
34	chr11:74557800-74560400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:74558200-74563400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr11:74558200-74564400	Strong transcription	Thymus	Thymus
37	chr11:74558200-74564600	Strong transcription	Dnd41	blood
38	chr11:74558200-74565200	Strong transcription	Colonic Mucosa	Colon
39	chr11:74558400-74564000	Strong transcription	Fetal Brain Female	brain
40	chr11:74558400-74564200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:74558400-74564600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr11:74558600-74560400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:74558600-74560800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr11:74558600-74561400	Weak transcription	Fetal Kidney	kidney
45	chr11:74558600-74561600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:74558600-74563400	Strong transcription	Brain Anterior Caudate	brain
47	chr11:74558600-74563400	Strong transcription	Left Ventricle	heart
48	chr11:74558600-74563600	Strong transcription	Placenta	Placenta
49	chr11:74558600-74565000	Strong transcription	Primary T cells from cord blood	blood
50	chr11:74558600-74565800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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