Variant report

Variant	rs56364420
Chromosome Location	chr11:93500659-93500660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:93500273..93502997-chr11:93515833..93518009,2	MCF-7	breast:
2	chr11:93500100..93501816-chr11:93503980..93506998,3	K562	blood:
3	chr11:93473222..93475738-chr11:93499019..93502627,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182919	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000042429	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10741476	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10765633	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10765634	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10831102	0.92[EUR][1000 genomes]
rs11020505	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11020506	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020507	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11020510	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11020521	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11020522	0.86[EUR][1000 genomes]
rs12292460	0.89[EUR][1000 genomes]
rs1284102	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1284108	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1284141	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1428919	0.92[EUR][1000 genomes]
rs1783938	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2077408	0.81[ASN][1000 genomes]
rs2434984	0.89[EUR][1000 genomes]
rs2848477	0.91[EUR][1000 genomes]
rs3132750	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132751	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4753103	0.90[EUR][1000 genomes]
rs585713	0.90[EUR][1000 genomes]
rs586293	0.93[EUR][1000 genomes]
rs588644	0.86[EUR][1000 genomes]
rs595650	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs598376	0.92[EUR][1000 genomes]
rs598427	0.85[EUR][1000 genomes]
rs602242	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs602665	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs606286	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs606357	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606462	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs606749	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs607615	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs611762	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs616876	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs618801	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs621355	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs622147	0.93[EUR][1000 genomes]
rs624856	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs625249	0.93[EUR][1000 genomes]
rs628661	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs630811	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs631177	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs631705	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs640379	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs640382	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs640864	0.92[EUR][1000 genomes]
rs644009	0.86[EUR][1000 genomes]
rs644535	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs652621	0.92[EUR][1000 genomes]
rs652961	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653939	0.99[EUR][1000 genomes]
rs655158	0.92[EUR][1000 genomes]
rs655699	0.86[EUR][1000 genomes]
rs658181	0.94[EUR][1000 genomes]
rs658698	0.88[EUR][1000 genomes]
rs658797	0.93[EUR][1000 genomes]
rs659877	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs662070	0.83[EUR][1000 genomes]
rs665507	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs666136	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs670871	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs673869	0.86[EUR][1000 genomes]
rs675441	0.92[EUR][1000 genomes]
rs675501	0.93[EUR][1000 genomes]
rs681321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs688634	0.94[EUR][1000 genomes]
rs693947	0.89[EUR][1000 genomes]
rs7943266	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7943525	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7950574	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs56364420	C11orf54	cis	Muscle Skeletal	GTEx
rs56364420	C11orf54	cis	Esophagus Mucosa	GTEx
rs56364420	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs56364420	C11orf54	cis	Adipose Subcutaneous	GTEx
rs56364420	C11orf54	cis	Artery Aorta	GTEx
rs56364420	C11orf54	cis	Thyroid	GTEx
rs56364420	C11orf54	cis	Whole Blood	GTEx
rs56364420	C11orf54	cis	Artery Tibial	GTEx
rs56364420	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs56364420	C11orf54	cis	Heart Left Ventricle	GTEx
rs56364420	C11orf54	cis	lung	GTEx
rs56364420	C11orf54	cis	Stomach	GTEx
rs56364420	C11orf54	cis	Nerve Tibial	GTEx
rs56364420	C11orf54	cis	Esophagus Muscularis	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93478800-93508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:93490200-93503200	Weak transcription	K562	blood
3	chr11:93490400-93501400	Weak transcription	HSMM	muscle
4	chr11:93492200-93503600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:93492200-93505400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:93492200-93505400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:93492200-93506600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:93492200-93507400	Weak transcription	Aorta	Aorta
9	chr11:93492200-93516600	Weak transcription	Psoas Muscle	Psoas
10	chr11:93492200-93516800	Weak transcription	Right Ventricle	heart
11	chr11:93492600-93501000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:93492600-93501600	Weak transcription	Brain Angular Gyrus	brain
13	chr11:93492800-93503200	Weak transcription	Colon Smooth Muscle	Colon
14	chr11:93493400-93505400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:93493800-93507200	Weak transcription	Ovary	ovary
16	chr11:93494000-93506200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:93495200-93505000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:93496000-93513600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:93497600-93501000	Weak transcription	Primary B cells from cord blood	blood
20	chr11:93497600-93505400	Weak transcription	Brain Germinal Matrix	brain
21	chr11:93497600-93506000	Weak transcription	Fetal Stomach	stomach
22	chr11:93497800-93504600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:93498000-93501400	Weak transcription	Left Ventricle	heart
24	chr11:93498000-93516600	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:93498200-93500800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:93498200-93505600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:93498400-93501800	Weak transcription	HSMMtube	muscle
28	chr11:93498600-93516600	Weak transcription	Hela-S3	cervix
29	chr11:93498800-93501800	Weak transcription	Spleen	Spleen
30	chr11:93498800-93503800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:93498800-93505400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:93498800-93506000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:93499000-93501200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:93499000-93501600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:93499000-93505200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:93499000-93505400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:93499000-93505800	Weak transcription	Fetal Muscle Leg	muscle
38	chr11:93499200-93505600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:93499200-93516600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:93499600-93506400	Weak transcription	Primary T cells from cord blood	blood
41	chr11:93499800-93505400	Weak transcription	Fetal Brain Female	brain
42	chr11:93499800-93516600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:93500000-93502600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:93500400-93500800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:93500400-93501000	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr11:93500400-93501600	Weak transcription	Stomach Mucosa	stomach
47	chr11:93500600-93501000	Weak transcription	Brain Substantia Nigra	brain
48	chr11:93500600-93501400	Weak transcription	Stomach Smooth Muscle	stomach

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