Variant report

Variant	rs529488
Chromosome Location	chr11:74673270-74673271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74672348..74674472-chr11:74684278..74686192,2	K562	blood:
2	chr11:74665537..74669916-chr11:74669929..74673689,6	K562	blood:
3	chr11:74662206..74664890-chr11:74672995..74675273,3	K562	blood:
4	chr11:74658629..74661558-chr11:74671465..74673618,3	K562	blood:
5	chr11:74672805..74674764-chr11:74674829..74677378,2	K562	blood:
6	chr11:74659294..74661127-chr11:74672207..74675302,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118363	Chromatin interaction
ENSG00000166435	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11236269	0.92[ASN][1000 genomes]
rs11605604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1282460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.81[ASN][1000 genomes]
rs1282689	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282690	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1282692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1282695	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1292895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1315297	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1583342	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2028343	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028344	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033532	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851136	0.85[ASN][1000 genomes]
rs2919057	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs41531051	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs471462	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs473080	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs473256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs480840	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[ASN][1000 genomes]
rs495246	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs502225	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs505688	0.86[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs508319	0.90[ASN][1000 genomes]
rs511021	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512780	0.86[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs519741	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527529	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs529249	0.92[ASN][1000 genomes]
rs537054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538502	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]
rs543244	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs546643	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs550869	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550980	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs557483	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs561589	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs562265	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567956	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs568758	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571446	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs577063	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs577102	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs580142	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590105	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs599722	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs614832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs616085	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624786	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643807	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs688665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs997465	0.80[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs529488	XRRA1	cis	Thyroid	GTEx
rs529488	XRRA1	cis	lymphoblastoid	seeQTL
rs529488	XRRA1	cis	Esophagus Mucosa	GTEx
rs529488	KRTAP5-10	cis	parietal	SCAN
rs529488	RNF169	cis	cerebellum	SCAN
rs529488	XRRA1	cis	Artery Tibial	GTEx
rs529488	RNF169	cis	lymphoblastoid	seeQTL
rs529488	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs529488	XRRA1	cis	Adipose Subcutaneous	GTEx
rs529488	XRRA1	cis	Muscle Skeletal	GTEx
rs529488	XRRA1	cis	cerebellum	SCAN
rs529488	XRRA1	cis	parietal	SCAN
rs529488	RP11-147I3.1	cis	Thyroid	GTEx
rs529488	XRRA1	cis	Whole Blood	GTEx
rs529488	XRRA1	cis	lung	GTEx
rs529488	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661200-74688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:74661600-74686000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:74661800-74675000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:74662000-74677600	Weak transcription	HSMMtube	muscle
7	chr11:74662000-74680800	Weak transcription	Fetal Kidney	kidney
8	chr11:74662000-74682200	Weak transcription	Aorta	Aorta
9	chr11:74662000-74682800	Weak transcription	Colonic Mucosa	Colon
10	chr11:74662200-74677000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:74662200-74677200	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:74662200-74677200	Weak transcription	Thymus	Thymus
13	chr11:74662200-74677800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:74662200-74677800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
16	chr11:74662400-74675200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:74662400-74677800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:74662400-74677800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:74662400-74677800	Weak transcription	Fetal Stomach	stomach
20	chr11:74662400-74680600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:74662400-74691400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:74662600-74676600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:74662600-74682800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:74662600-74686000	Weak transcription	Fetal Brain Male	brain
25	chr11:74662800-74677800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:74662800-74682200	Weak transcription	Lung	lung
27	chr11:74663200-74680000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:74664000-74680400	Weak transcription	HMEC	breast
29	chr11:74664200-74677200	Weak transcription	Fetal Lung	lung
30	chr11:74664400-74675800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr11:74664400-74678000	Weak transcription	Brain Germinal Matrix	brain
32	chr11:74664600-74675800	Weak transcription	Fetal Intestine Large	intestine
33	chr11:74664600-74677800	Weak transcription	NHLF	lung
34	chr11:74665600-74686000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:74665800-74675800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:74666200-74674800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr11:74666200-74677200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:74666600-74674200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:74666600-74675800	Weak transcription	A549	lung
40	chr11:74667600-74689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:74667800-74674800	Weak transcription	Fetal Thymus	thymus
42	chr11:74667800-74677800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:74667800-74678400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:74667800-74683200	Weak transcription	Small Intestine	intestine
45	chr11:74667800-74692200	Strong transcription	Dnd41	blood
46	chr11:74668000-74673600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr11:74668000-74677800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:74668000-74680800	Weak transcription	Brain Angular Gyrus	brain
49	chr11:74668200-74673800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:74668600-74674600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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