Variant report

Variant	rs628661
Chromosome Location	chr11:93498126-93498127
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:93474520..93476254-chr11:93496960..93498891,2	MCF-7	breast:
2	chr11:93476133..93478547-chr11:93497585..93500296,2	K562	blood:
3	chr11:93487232..93489267-chr11:93497317..93499551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166012	Chromatin interaction
ENSG00000182919	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10741476	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10765633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10765634	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10831102	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11020505	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11020506	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11020507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11020510	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11020521	0.88[EUR][1000 genomes]
rs11020522	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12292460	0.90[EUR][1000 genomes]
rs12803773	0.89[AFR][1000 genomes]
rs1284102	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1284108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1284141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1428919	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1783938	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2434978	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2434984	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2510603	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2848477	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132751	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4753103	0.91[EUR][1000 genomes]
rs56364420	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs585713	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs586293	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs588644	0.86[EUR][1000 genomes]
rs595650	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598376	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs598427	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs601711	0.80[EUR][1000 genomes]
rs602242	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs602665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs606286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606357	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs606462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607615	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs611762	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs616876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618801	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs621355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs622147	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs624856	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625249	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs630811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631177	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs631705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640379	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs640382	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs640864	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs644009	0.86[EUR][1000 genomes]
rs644535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6483265	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs652621	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs652961	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs653939	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs655158	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs655699	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs658181	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs658698	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs658797	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs659877	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs662070	0.84[EUR][1000 genomes]
rs665507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs670871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs673869	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs675441	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs675501	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs681321	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs688634	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs693947	0.90[EUR][1000 genomes]
rs7943266	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7943525	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950574	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs628661	C11orf54	cis	Artery Aorta	GTEx
rs628661	C11orf54	cis	Muscle Skeletal	GTEx
rs628661	C11orf54	cis	Stomach	GTEx
rs628661	C11orf54	cis	Heart Left Ventricle	GTEx
rs628661	C11orf54	cis	Esophagus Mucosa	GTEx
rs628661	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs628661	C11orf54	cis	Thyroid	GTEx
rs628661	C11orf54	cis	Nerve Tibial	GTEx
rs628661	C11orf54	cis	multi-tissue	Pritchard
rs628661	C11orf54	cis	Esophagus Muscularis	GTEx
rs628661	C11orf54	cis	Whole Blood	GTEx
rs628661	C11orf54	cis	Artery Tibial	GTEx
rs628661	C11orf54	cis	Adipose Subcutaneous	GTEx
rs628661	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs628661	C11orf54	cis	lung	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93476000-93498800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr11:93476200-93499800	Weak transcription	NH-A	brain
3	chr11:93478200-93498800	Weak transcription	Fetal Heart	heart
4	chr11:93478600-93498200	Weak transcription	Stomach Mucosa	stomach
5	chr11:93478800-93508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:93482000-93499600	Weak transcription	NHEK	skin
7	chr11:93482400-93499200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:93482800-93498400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:93484800-93498200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:93485000-93498600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr11:93485000-93499800	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:93485400-93498600	Strong transcription	Fetal Thymus	thymus
13	chr11:93486000-93499000	Strong transcription	Fetal Muscle Leg	muscle
14	chr11:93486600-93498800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:93486600-93499000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:93486600-93499000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:93486600-93499000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr11:93486800-93498200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:93486800-93499200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:93488200-93498200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:93488200-93498600	Strong transcription	Thymus	Thymus
22	chr11:93488200-93499200	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:93488400-93499000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:93488800-93498800	Weak transcription	Fetal Brain Male	brain
25	chr11:93489600-93499000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:93490200-93503200	Weak transcription	K562	blood
27	chr11:93490400-93498400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:93490400-93501400	Weak transcription	HSMM	muscle
29	chr11:93491000-93499800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:93492000-93498800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:93492000-93499400	Weak transcription	NHLF	lung
32	chr11:93492200-93498800	Strong transcription	Fetal Intestine Large	intestine
33	chr11:93492200-93499400	Weak transcription	Gastric	stomach
34	chr11:93492200-93499400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:93492200-93499800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:93492200-93500400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:93492200-93500400	Weak transcription	Brain Substantia Nigra	brain
38	chr11:93492200-93503600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr11:93492200-93505400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:93492200-93505400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:93492200-93506600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr11:93492200-93507400	Weak transcription	Aorta	Aorta
43	chr11:93492200-93516600	Weak transcription	Psoas Muscle	Psoas
44	chr11:93492200-93516800	Weak transcription	Right Ventricle	heart
45	chr11:93492400-93499000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:93492600-93501000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr11:93492600-93501600	Weak transcription	Brain Angular Gyrus	brain
48	chr11:93492800-93503200	Weak transcription	Colon Smooth Muscle	Colon
49	chr11:93493200-93498800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:93493400-93499000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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