Variant report

Variant	rs2742486
Chromosome Location	chr11:8984378-8984379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:8984369-8987031	GM12891	blood:	n/a	n/a
2	ATF1	chr11:8984050-8984701	K562	blood:	n/a	n/a
3	TAL1	chr11:8984357-8984810	K562	blood:	n/a	n/a
4	TEAD4	chr11:8984285-8984806	K562	blood:	n/a	n/a
5	TEAD4	chr11:8984285-8984785	K562	blood:	n/a	n/a
6	POLR2A	chr11:8983991-8986899	PBDE	blood:	n/a	n/a
7	SPI1	chr11:8984353-8984530	K562	blood:	n/a	n/a
8	GATA1	chr11:8983930-8985414	PBDE	blood:	n/a	chr11:8985252-8985262 chr11:8984461-8984470
9	RCOR1	chr11:8984316-8984684	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:8983362..8985132-chr11:9043437..9045026,2	K562	blood:
2	chr11:8983863..8986997-chr11:9158044..9162292,6	MCF-7	breast:
3	chr11:8977155..8979531-chr11:8982227..8985372,3	MCF-7	breast:
4	chr11:8984349..8987280-chr11:9024480..9026486,3	K562	blood:
5	chr11:8931659..8933906-chr11:8984325..8986430,2	K562	blood:
6	chr11:8976172..8977812-chr11:8982786..8984481,2	K562	blood:

No data

Variant related genes	Relation type
TMEM9B-AS1	TF binding region
ENSG00000175356	Chromatin interaction
ENSG00000253973	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000175352	Chromatin interaction
ENSG00000166452	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10219366	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1025438	0.80[ASN][1000 genomes]
rs10734639	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10743094	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10769974	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10769976	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10769977	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840151	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840153	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840154	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840155	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840156	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042128	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042129	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042131	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12785559	0.87[ASN][1000 genomes]
rs12786377	0.87[ASN][1000 genomes]
rs12790020	0.87[ASN][1000 genomes]
rs12794962	0.87[ASN][1000 genomes]
rs12798311	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12805109	0.87[ASN][1000 genomes]
rs1347016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985026	0.87[ASN][1000 genomes]
rs2016844	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2043218	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2056903	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2116510	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116511	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163625	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246878	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247038	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2252102	0.89[ASN][1000 genomes]
rs2316523	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2316541	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568047	0.87[ASN][1000 genomes]
rs2568069	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568074	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568075	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568077	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568079	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568081	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568086	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568087	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568088	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653587	0.88[AFR][1000 genomes]
rs2653590	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653594	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2653597	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2653601	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653604	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653611	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742473	0.87[ASN][1000 genomes]
rs2742487	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742488	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742489	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742491	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742493	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742494	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2742495	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742496	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742497	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742504	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742505	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742512	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742513	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742514	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742519	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751063	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3751065	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3751066	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3751068	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3763911	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3763912	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4370967	0.83[ASN][1000 genomes]
rs4909951	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4910313	0.87[ASN][1000 genomes]
rs7106152	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7124403	0.87[ASN][1000 genomes]
rs72851596	0.88[ASN][1000 genomes]
rs72852790	0.98[ASN][1000 genomes]
rs72853712	0.98[ASN][1000 genomes]
rs7932377	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7940895	0.91[ASN][1000 genomes]
rs7942026	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7951226	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs909464	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9300096	0.83[AMR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2742486	C11orf17	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:8954400-8984400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:8963200-8985000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:8965800-8984800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:8968200-8985000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:8970600-8984400	Weak transcription	Right Ventricle	heart
7	chr11:8970600-8985000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:8970800-8984400	Weak transcription	A549	lung
9	chr11:8971200-8984400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:8973600-8985000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:8974800-8984400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:8977400-8984800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:8977600-8985000	Weak transcription	Esophagus	oesophagus
14	chr11:8977600-8985000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:8977800-8984400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:8977800-8984400	Weak transcription	Fetal Thymus	thymus
17	chr11:8978000-8984400	Weak transcription	Spleen	Spleen
18	chr11:8978000-8985000	Weak transcription	Gastric	stomach
19	chr11:8978000-8985000	Weak transcription	Lung	lung
20	chr11:8978600-8984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:8978800-8984600	Weak transcription	Placenta	Placenta
22	chr11:8979200-8984400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:8979400-8984400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:8981000-8984400	Weak transcription	Pancreas	Pancrea
25	chr11:8981000-8984800	Weak transcription	Right Atrium	heart
26	chr11:8981000-8985000	Weak transcription	Left Ventricle	heart
27	chr11:8981200-8984400	Weak transcription	Fetal Heart	heart
28	chr11:8981200-8984600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:8981200-8984600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:8981200-8985200	Weak transcription	Ovary	ovary
31	chr11:8981400-8984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:8981600-8984400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:8981600-8984400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr11:8981600-8984400	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:8981600-8984400	Weak transcription	Brain Substantia Nigra	brain
36	chr11:8981600-8984400	Weak transcription	Fetal Muscle Leg	muscle
37	chr11:8981600-8984400	Weak transcription	Fetal Stomach	stomach
38	chr11:8981600-8984400	Weak transcription	HSMMtube	muscle
39	chr11:8981600-8984600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:8981600-8984800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:8981600-8984800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr11:8981600-8984800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:8981600-8984800	Weak transcription	Fetal Kidney	kidney
44	chr11:8981600-8985000	Weak transcription	Aorta	Aorta
45	chr11:8982000-8984800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:8982800-8984400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:8982800-8987000	Active TSS	GM12878-XiMat	blood
48	chr11:8983000-8984400	Enhancers	Brain Cingulate Gyrus	brain
49	chr11:8983000-8984600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr11:8983000-8984800	Enhancers	Liver	Liver

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