Variant report

Variant	rs543244
Chromosome Location	chr11:74654792-74654793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74646789..74652263-chr11:74653149..74657657,8	K562	blood:
2	chr11:74644656..74646769-chr11:74653647..74656340,2	MCF-7	breast:
3	chr11:74648814..74655241-chr11:74658566..74662539,10	MCF-7	breast:
4	chr11:74640134..74643076-chr11:74654287..74656297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118363	Chromatin interaction
ENSG00000166435	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs11236269	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11605604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1282460	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];0.85[ASN][1000 genomes]
rs1282461	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1282689	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282690	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282695	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1292895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1303525	0.81[AMR][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1583342	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033532	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851136	0.83[ASN][1000 genomes]
rs2919057	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs41531051	0.89[AFR][1000 genomes];0.97[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	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs473080	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480840	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs483615	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs495246	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs497772	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs502225	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs505688	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes]
rs508319	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512780	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs519741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527529	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs529249	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs529488	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]
rs537054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs538502	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	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550980	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs557483	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561589	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs562265	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565767	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs567956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568758	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571446	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573925	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577063	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577102	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs580142	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590105	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614832	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];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616085	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624786	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625268	1.00[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];0.85[ASN][1000 genomes]
rs629573	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643807	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997465	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.84[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs543244	XRRA1	cis	Artery Tibial	GTEx
rs543244	RNF169	cis	multi-tissue	Pritchard
rs543244	RNF169	cis	cerebellum	SCAN
rs543244	XRRA1	cis	Whole Blood	GTEx
rs543244	KRTAP5-10	cis	parietal	SCAN
rs543244	XRRA1	cis	lung	GTEx
rs543244	RP11-147I3.1	cis	Thyroid	GTEx
rs543244	RNF169	cis	lymphoblastoid	seeQTL
rs543244	XRRA1	cis	lymphoblastoid	seeQTL
rs543244	XRRA1	cis	multi-tissue	Pritchard
rs543244	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs543244	XRRA1	cis	cerebellum	SCAN
rs543244	XRRA1	cis	parietal	SCAN
rs543244	XRRA1	cis	Esophagus Mucosa	GTEx
rs543244	XRRA1	cis	Muscle Skeletal	GTEx
rs543244	XRRA1	cis	Thyroid	GTEx
rs543244	XRRA1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
2	chr11:74618000-74659600	Weak transcription	Esophagus	oesophagus
3	chr11:74620400-74659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:74627800-74659200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:74628200-74659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:74630800-74659000	Weak transcription	Fetal Brain Male	brain
7	chr11:74631600-74659000	Weak transcription	Hela-S3	cervix
8	chr11:74632200-74659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:74633000-74659400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:74636000-74656200	Strong transcription	Fetal Intestine Large	intestine
11	chr11:74636000-74658200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr11:74637400-74656400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr11:74637800-74655400	Strong transcription	Fetal Stomach	stomach
14	chr11:74641600-74659000	Weak transcription	A549	lung
15	chr11:74642000-74659400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:74642000-74659600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:74642400-74656000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:74642600-74656200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr11:74642800-74655600	Strong transcription	Placenta	Placenta
20	chr11:74643400-74655200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:74644200-74659400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:74646600-74659200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr11:74647600-74659000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:74648000-74659000	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:74648000-74659200	Weak transcription	Brain Substantia Nigra	brain
26	chr11:74648000-74659400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:74648000-74659400	Weak transcription	Fetal Brain Female	brain
28	chr11:74648000-74659600	Weak transcription	Pancreas	Pancrea
29	chr11:74648000-74659600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:74648000-74659600	Weak transcription	Spleen	Spleen
31	chr11:74648200-74655000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:74648200-74659000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:74648200-74659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:74648200-74659600	Weak transcription	Brain Germinal Matrix	brain
35	chr11:74648200-74659600	Weak transcription	Fetal Thymus	thymus
36	chr11:74648200-74659600	Weak transcription	Left Ventricle	heart
37	chr11:74648400-74655200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:74648400-74659200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:74648400-74659200	Weak transcription	Right Ventricle	heart
40	chr11:74648400-74659600	Weak transcription	Fetal Heart	heart
41	chr11:74648600-74659200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr11:74648600-74659600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:74648800-74659200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr11:74649600-74655000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:74649800-74659000	Weak transcription	GM12878-XiMat	blood
46	chr11:74650000-74659200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:74650200-74659200	Weak transcription	HUVEC	blood vessel
48	chr11:74650600-74656000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:74650800-74656400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr11:74651400-74659400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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