Variant report

Variant	rs546643
Chromosome Location	chr11:74655107-74655108
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	chr11:74654949..74658411-chr11:74658805..74662988,5	MCF-7	breast:
4	chr11:74648814..74655241-chr11:74658566..74662539,10	MCF-7	breast:
5	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: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11236269	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605604	0.92[ASN][1000 genomes]
rs12363224	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1282460	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1282461	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282689	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282690	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282692	0.94[ASN][1000 genomes]
rs1282695	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1292895	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1297319	0.98[ASN][1000 genomes]
rs1303525	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1315297	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1583342	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2028343	0.98[ASN][1000 genomes]
rs2028344	0.98[ASN][1000 genomes]
rs2033532	0.88[AMR][1000 genomes]
rs2851136	0.83[ASN][1000 genomes]
rs2919057	0.83[ASN][1000 genomes]
rs41531051	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs471462	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs473080	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs480840	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs483615	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs495246	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs497772	0.80[AFR][1000 genomes]
rs502225	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs505688	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs508319	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511021	0.98[ASN][1000 genomes]
rs511890	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512780	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs513137	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs519741	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527529	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs529249	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs529488	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537054	0.93[ASN][1000 genomes]
rs538502	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs543244	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550491	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs550869	0.98[ASN][1000 genomes]
rs550980	0.92[ASN][1000 genomes]
rs557483	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs561589	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs562265	1.00[ASN][1000 genomes]
rs565767	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs567956	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568558	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs568758	0.98[ASN][1000 genomes]
rs571446	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs573925	0.94[ASN][1000 genomes]
rs577063	0.94[ASN][1000 genomes]
rs577102	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs580142	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs590105	0.94[ASN][1000 genomes]
rs599722	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs603062	0.94[ASN][1000 genomes]
rs614832	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616085	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624786	0.93[ASN][1000 genomes]
rs625268	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs629573	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641584	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643807	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646287	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs688665	1.00[ASN][1000 genomes]
rs9444	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs997465	0.81[AMR][1000 genomes];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs546643	XRRA1	cis	Muscle Skeletal	GTEx
rs546643	XRRA1	cis	Whole Blood	GTEx
rs546643	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 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	chr11:74648200-74659000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:74648200-74659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:74648200-74659600	Weak transcription	Brain Germinal Matrix	brain
34	chr11:74648200-74659600	Weak transcription	Fetal Thymus	thymus
35	chr11:74648200-74659600	Weak transcription	Left Ventricle	heart
36	chr11:74648400-74655200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:74648400-74659200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:74648400-74659200	Weak transcription	Right Ventricle	heart
39	chr11:74648400-74659600	Weak transcription	Fetal Heart	heart
40	chr11:74648600-74659200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr11:74648600-74659600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:74648800-74659200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:74649800-74659000	Weak transcription	GM12878-XiMat	blood
44	chr11:74650000-74659200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:74650200-74659200	Weak transcription	HUVEC	blood vessel
46	chr11:74650600-74656000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:74650800-74656400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr11:74651400-74659400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:74651600-74656000	Strong transcription	Thymus	Thymus
50	chr11:74651600-74659400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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