Variant report

Variant	rs2568075
Chromosome Location	chr11:8949094-8949095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8940620..8943003-chr11:8946457..8949397,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASCL3-1	chr11:8949050-8949255	NONHSAT017890

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10219366	0.95[EUR][1000 genomes]
rs1025438	0.85[ASN][1000 genomes]
rs10734639	0.83[EUR][1000 genomes]
rs10743094	0.83[EUR][1000 genomes]
rs10769974	0.83[EUR][1000 genomes]
rs10769976	0.96[EUR][1000 genomes]
rs10769977	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10840150	0.87[EUR][1000 genomes]
rs10840151	0.81[EUR][1000 genomes]
rs10840153	0.81[EUR][1000 genomes]
rs10840154	0.81[EUR][1000 genomes]
rs10840155	0.81[EUR][1000 genomes]
rs10840156	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11042121	0.88[EUR][1000 genomes]
rs11042131	0.81[EUR][1000 genomes]
rs12785559	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12786377	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12790020	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12794962	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12798311	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12805109	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1347016	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985026	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2016844	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2043218	0.80[EUR][1000 genomes]
rs2056903	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2116510	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2116511	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2163625	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2246878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252102	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2316541	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568034	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2568042	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2568047	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568069	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568079	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568081	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568086	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568087	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568088	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2653556	0.83[EUR][1000 genomes]
rs2653562	0.84[EUR][1000 genomes]
rs2653565	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2653587	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2653590	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653597	0.88[ASN][1000 genomes]
rs2653601	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653604	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653611	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742473	0.81[ASN][1000 genomes]
rs2742486	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742487	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742488	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742489	0.86[ASN][1000 genomes]
rs2742491	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742493	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742495	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742496	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742497	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742504	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742505	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742512	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742513	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742514	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742519	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742520	0.83[EUR][1000 genomes]
rs2742521	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3751063	0.96[EUR][1000 genomes]
rs3751065	0.83[EUR][1000 genomes]
rs3751066	0.83[EUR][1000 genomes]
rs3751068	0.83[EUR][1000 genomes]
rs3763911	0.81[EUR][1000 genomes]
rs3763912	0.81[EUR][1000 genomes]
rs4370967	0.80[EUR][1000 genomes]
rs4909951	0.96[EUR][1000 genomes]
rs4910181	0.91[EUR][1000 genomes]
rs4910313	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7106152	0.81[EUR][1000 genomes]
rs7106539	0.82[EUR][1000 genomes]
rs7124403	0.81[ASN][1000 genomes]
rs72851596	0.93[ASN][1000 genomes]
rs72852790	0.93[ASN][1000 genomes]
rs72853712	0.93[ASN][1000 genomes]
rs7932377	0.81[EUR][1000 genomes]
rs7940895	0.86[ASN][1000 genomes]
rs7951226	0.81[EUR][1000 genomes]
rs909464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9300096	0.96[EUR][1000 genomes]
rs982273	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers 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 target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2568075	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs2568075	C11orf17	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
3	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:8940200-8949200	Weak transcription	Primary B cells from cord blood	blood
5	chr11:8940800-8949200	Weak transcription	Fetal Heart	heart
6	chr11:8941200-8953400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:8941200-8956200	Weak transcription	K562	blood
8	chr11:8942400-8950200	Weak transcription	Esophagus	oesophagus
9	chr11:8942400-8959000	Weak transcription	Fetal Kidney	kidney
10	chr11:8943200-8950000	Weak transcription	GM12878-XiMat	blood
11	chr11:8943200-8950800	Weak transcription	Primary T cells from cord blood	blood
12	chr11:8943800-8969200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:8944000-8952200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:8944200-8956400	Weak transcription	HUVEC	blood vessel
15	chr11:8944600-8950000	Weak transcription	HMEC	breast
16	chr11:8944600-8950000	Weak transcription	HSMMtube	muscle
17	chr11:8944600-8950800	Weak transcription	HepG2	liver
18	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:8944800-8949200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:8944800-8949600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:8944800-8950200	Weak transcription	Placenta	Placenta
22	chr11:8944800-8954000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:8944800-8956400	Weak transcription	Fetal Intestine Large	intestine
24	chr11:8945000-8949800	Weak transcription	Pancreas	Pancrea
25	chr11:8945000-8950200	Weak transcription	Right Ventricle	heart
26	chr11:8945000-8950400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:8945000-8950400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:8945000-8950400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:8945000-8950400	Weak transcription	HSMM	muscle
30	chr11:8945000-8950400	Weak transcription	Osteobl	bone
31	chr11:8945000-8950800	Weak transcription	Brain Substantia Nigra	brain
32	chr11:8945000-8950800	Weak transcription	Ovary	ovary
33	chr11:8945000-8951000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:8945000-8951800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:8945000-8953600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:8945000-8953600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:8945000-8954000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:8945000-8954000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:8945000-8955000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:8945000-8956200	Weak transcription	NH-A	brain
41	chr11:8945200-8954000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:8945200-8954400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:8945200-8956200	Weak transcription	A549	lung
44	chr11:8945600-8950200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:8945800-8954800	Weak transcription	Hela-S3	cervix
46	chr11:8945800-8974000	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:8946200-8950400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:8946400-8950200	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:8946400-8950400	Weak transcription	NHEK	skin
50	chr11:8946400-8956200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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