Variant report

Variant	rs564587
Chromosome Location	chr11:62505037-62505038
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62504535..62506343-chr11:62516715..62519641,2	K562	blood:
2	chr11:62504502..62506566-chr11:62646418..62648273,2	K562	blood:
3	chr11:62503534..62505180-chr11:62608140..62610397,2	K562	blood:
4	chr11:62499024..62507318-chr11:62604678..62610455,13	MCF-7	breast:
5	chr11:62503362..62506102-chr11:62571092..62572818,2	MCF-7	breast:
6	chr11:62495253..62497354-chr11:62504710..62507257,3	MCF-7	breast:
7	chr11:62500518..62507069-chr11:62517079..62523179,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162231	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000185670	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11822922	1.00[EUR][1000 genomes]
rs12273912	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1787724	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2510538	1.00[EUR][1000 genomes]
rs2584915	0.82[ASW][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2584917	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2730030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2730033	1.00[AMR][1000 genomes]
rs2956139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2958240	1.00[EUR][1000 genomes]
rs4387351	1.00[TSI][hapmap]
rs481272	0.82[ASW][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs482331	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs486451	0.82[ASW][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs489275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4963309	0.82[ASW][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs506132	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs507101	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs514401	1.00[EUR][1000 genomes]
rs518780	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs519473	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs560006	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs560603	1.00[AMR][1000 genomes]
rs560618	1.00[EUR][1000 genomes]
rs561385	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs561520	1.00[AMR][1000 genomes]
rs56226867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs572513	0.82[ASW][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs573146	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57338459	1.00[EUR][1000 genomes]
rs575134	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs577071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57858466	1.00[EUR][1000 genomes]
rs592337	0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs595108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs646194	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs692773	1.00[EUR][1000 genomes]
rs694678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73487819	1.00[AMR][1000 genomes]
rs73487834	1.00[EUR][1000 genomes]
rs73487878	1.00[EUR][1000 genomes]
rs73487879	1.00[EUR][1000 genomes]
rs73487880	1.00[EUR][1000 genomes]
rs73490026	1.00[EUR][1000 genomes]
rs73502133	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
5	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
6	nsv348	chr11:62474450-62519712	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs564587	C11orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62496800-62516400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:62496800-62521000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:62497000-62508200	Weak transcription	Aorta	Aorta
4	chr11:62497400-62520400	Weak transcription	Psoas Muscle	Psoas
5	chr11:62497600-62519400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:62497800-62509600	Strong transcription	Fetal Intestine Small	intestine
7	chr11:62497800-62519600	Weak transcription	Gastric	stomach
8	chr11:62498000-62505600	Weak transcription	Small Intestine	intestine
9	chr11:62498000-62505800	Weak transcription	Right Ventricle	heart
10	chr11:62498000-62509600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:62498000-62509600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:62498000-62509600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:62498600-62509600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:62498800-62505800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:62498800-62509200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:62498800-62509600	Strong transcription	Fetal Stomach	stomach
17	chr11:62499000-62509600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:62499000-62520800	Weak transcription	Fetal Brain Male	brain
19	chr11:62499200-62509600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr11:62499200-62520800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:62499400-62510200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:62500000-62509000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:62500200-62509000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:62500200-62509200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:62500200-62509400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:62500200-62509400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:62500200-62509800	Strong transcription	Fetal Muscle Leg	muscle
28	chr11:62500400-62507600	Strong transcription	Fetal Brain Female	brain
29	chr11:62500400-62508400	Strong transcription	Dnd41	blood
30	chr11:62500400-62508800	Strong transcription	Fetal Intestine Large	intestine
31	chr11:62500400-62509000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:62500400-62509000	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr11:62500400-62509200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:62500400-62509400	Strong transcription	Liver	Liver
35	chr11:62500400-62509400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:62500400-62509600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:62500400-62509600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:62500400-62509800	Strong transcription	Fetal Thymus	thymus
39	chr11:62500600-62506200	Strong transcription	Primary B cells from cord blood	blood
40	chr11:62500600-62508400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr11:62500600-62508600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:62500600-62509200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr11:62500600-62509600	Strong transcription	Osteobl	bone
44	chr11:62500600-62510600	Strong transcription	Thymus	Thymus
45	chr11:62500800-62508200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:62500800-62508400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:62500800-62508400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:62500800-62509200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:62500800-62509200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:62500800-62509200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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