Variant report

Variant	rs508319
Chromosome Location	chr11:74637077-74637078
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr11:74637057-74637798	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74636188..74638318-chr11:74659993..74661874,2	MCF-7	breast:
2	chr11:74628676..74630769-chr11:74635809..74638520,2	MCF-7	breast:

Variant related genes	Relation type
XRRA1	TF binding region
ENSG00000166435	Chromatin interaction
ENSG00000241170	Chromatin interaction
ENSG00000118363	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11236269	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605604	0.96[ASN][1000 genomes]
rs12363224	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1282460	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1282461	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282689	0.92[ASN][1000 genomes]
rs1282690	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1282692	0.86[ASN][1000 genomes]
rs1282695	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1292895	0.92[ASN][1000 genomes]
rs1297319	0.90[ASN][1000 genomes]
rs1303525	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1315297	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1583342	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2028343	0.90[ASN][1000 genomes]
rs2028344	0.90[ASN][1000 genomes]
rs2033532	0.88[AMR][1000 genomes]
rs41531051	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs471462	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs473080	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs480840	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs483615	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs495246	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs497772	0.83[AFR][1000 genomes]
rs502225	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs505688	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs511021	0.90[ASN][1000 genomes]
rs511890	0.90[ASN][1000 genomes]
rs512780	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs513137	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs519741	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs527529	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529249	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529488	0.90[ASN][1000 genomes]
rs537054	0.85[ASN][1000 genomes]
rs538502	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs543244	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs546643	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550491	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs550869	0.90[ASN][1000 genomes]
rs550980	0.96[ASN][1000 genomes]
rs557483	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs561589	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs562265	0.92[ASN][1000 genomes]
rs565767	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs567956	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs568558	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568758	0.90[ASN][1000 genomes]
rs571446	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs573925	0.98[ASN][1000 genomes]
rs577063	0.86[ASN][1000 genomes]
rs577102	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs580142	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs590105	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599722	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs603062	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs614832	0.92[ASN][1000 genomes]
rs616085	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs624786	0.85[ASN][1000 genomes]
rs625268	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs629573	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs641584	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs643807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646287	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688665	0.92[ASN][1000 genomes]
rs9444	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs997465	0.81[AMR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs508319	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs508319	XRRA1	cis	Muscle Skeletal	GTEx
rs508319	XRRA1	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
2	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
3	chr11:74613800-74637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:74615200-74637200	Weak transcription	HMEC	breast
5	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:74616400-74646000	Weak transcription	Spleen	Spleen
7	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
8	chr11:74617400-74648200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:74618000-74659600	Weak transcription	Esophagus	oesophagus
10	chr11:74618400-74653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:74619200-74639800	Weak transcription	K562	blood
12	chr11:74620000-74646200	Weak transcription	Right Ventricle	heart
13	chr11:74620400-74659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:74624200-74643200	Weak transcription	HSMMtube	muscle
15	chr11:74627800-74659200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:74628200-74659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:74628400-74640800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr11:74629400-74637200	Weak transcription	GM12878-XiMat	blood
19	chr11:74630000-74643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:74630000-74645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:74630000-74646000	Weak transcription	Aorta	Aorta
22	chr11:74630200-74643400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:74630400-74644600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:74630800-74637200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr11:74630800-74639000	Weak transcription	Fetal Lung	lung
26	chr11:74630800-74646000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:74630800-74659000	Weak transcription	Fetal Brain Male	brain
28	chr11:74631000-74646000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:74631600-74659000	Weak transcription	Hela-S3	cervix
30	chr11:74632000-74640600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr11:74632200-74637400	Weak transcription	Brain Substantia Nigra	brain
32	chr11:74632200-74643400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:74632200-74644000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:74632200-74646000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:74632200-74659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:74632400-74639400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:74632400-74643200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:74632400-74643400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:74632400-74643400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:74632400-74643600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:74632400-74644200	Weak transcription	Fetal Thymus	thymus
42	chr11:74632400-74644800	Weak transcription	Fetal Brain Female	brain
43	chr11:74632400-74645600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr11:74632400-74646000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:74632400-74646000	Weak transcription	Brain Germinal Matrix	brain
46	chr11:74632400-74647200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:74632400-74647200	Weak transcription	Lung	lung
48	chr11:74632400-74648400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:74632600-74637800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:74632600-74638000	Weak transcription	Liver	Liver

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