Variant report

Variant	rs12798311
Chromosome Location	chr11:8934988-8934989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:8934786-8935045	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:8934819..8937365-chr11:8941717..8944369,2	K562	blood:
2	chr11:8932596..8934469-chr11:8934808..8936495,2	MCF-7	breast:
3	chr11:8709217..8711333-chr11:8934595..8937178,2	MCF-7	breast:
4	chr11:8701763..8703828-chr11:8934006..8936271,2	K562	blood:
5	chr11:8712215..8714254-chr11:8934195..8936009,2	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000166441	Chromatin interaction
ENSG00000166452	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10219366	0.95[EUR][1000 genomes]
rs1025438	0.86[ASN][1000 genomes]
rs10734639	0.83[EUR][1000 genomes]
rs10743094	0.83[EUR][1000 genomes]
rs10769974	0.83[EUR][1000 genomes]
rs10769976	0.95[EUR][1000 genomes]
rs10769977	0.80[EUR][1000 genomes]
rs10840150	0.87[EUR][1000 genomes]
rs10840151	0.80[EUR][1000 genomes]
rs10840153	0.80[EUR][1000 genomes]
rs10840154	0.80[EUR][1000 genomes]
rs10840155	0.80[EUR][1000 genomes]
rs10840156	0.96[EUR][1000 genomes]
rs11042121	0.89[EUR][1000 genomes]
rs11042131	0.80[EUR][1000 genomes]
rs12805109	0.80[EUR][1000 genomes]
rs1347016	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2016844	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2056903	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2116510	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2116511	0.89[ASN][1000 genomes]
rs2163625	0.80[EUR][1000 genomes]
rs2246878	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247038	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252102	0.82[EUR][1000 genomes]
rs2316541	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568034	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568042	0.94[EUR][1000 genomes]
rs2568047	0.80[EUR][1000 genomes]
rs2568069	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568074	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568075	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568077	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568079	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568081	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568086	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568087	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568088	0.83[ASN][1000 genomes]
rs2653556	0.84[EUR][1000 genomes]
rs2653562	0.85[EUR][1000 genomes]
rs2653565	0.94[EUR][1000 genomes]
rs2653587	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2653590	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2653597	0.84[ASN][1000 genomes]
rs2653601	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653604	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2653611	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742486	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742487	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742488	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742489	0.83[ASN][1000 genomes]
rs2742491	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742493	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742495	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2742496	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742497	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742504	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742505	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742512	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742513	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742514	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742519	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742520	0.83[EUR][1000 genomes]
rs2742521	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3751063	0.95[EUR][1000 genomes]
rs3751065	0.82[EUR][1000 genomes]
rs3751066	0.83[EUR][1000 genomes]
rs3751068	0.83[EUR][1000 genomes]
rs3763911	0.80[EUR][1000 genomes]
rs3763912	0.80[EUR][1000 genomes]
rs4909951	0.95[EUR][1000 genomes]
rs4910181	0.91[EUR][1000 genomes]
rs7106152	0.80[EUR][1000 genomes]
rs7106539	0.83[EUR][1000 genomes]
rs72851596	0.94[ASN][1000 genomes]
rs72852790	0.89[ASN][1000 genomes]
rs72853712	0.89[ASN][1000 genomes]
rs7932377	0.80[EUR][1000 genomes]
rs7940895	0.83[ASN][1000 genomes]
rs7951226	0.80[EUR][1000 genomes]
rs909464	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9300096	0.95[EUR][1000 genomes]
rs982273	0.84[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
rs12798311	C11orf17	cis	multi-tissue	Pritchard
rs12798311	C11orf17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8931600-8935200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:8933400-8935000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:8933400-8935000	Weak transcription	Gastric	stomach
4	chr11:8933400-8935000	Weak transcription	Spleen	Spleen
5	chr11:8933400-8935200	Weak transcription	Stomach Mucosa	stomach
6	chr11:8933400-8935800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:8933400-8936400	Weak transcription	Lung	lung
8	chr11:8933400-8938000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
10	chr11:8933600-8935400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:8933600-8935600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr11:8933600-8935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:8933600-8938000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:8933600-8944000	Weak transcription	Pancreas	Pancrea
15	chr11:8933800-8935000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr11:8933800-8935000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:8933800-8935200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:8934000-8935400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr11:8934000-8935600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:8934000-8935600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:8934000-8935600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr11:8934000-8935600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr11:8934000-8935600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:8934000-8935800	Enhancers	Right Atrium	heart
25	chr11:8934000-8938000	Weak transcription	Fetal Intestine Large	intestine
26	chr11:8934000-8941800	Weak transcription	Colonic Mucosa	Colon
27	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:8934200-8935000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:8934200-8935000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:8934200-8935000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:8934200-8935000	Weak transcription	Fetal Intestine Small	intestine
32	chr11:8934200-8935000	Enhancers	Fetal Muscle Leg	muscle
33	chr11:8934200-8935000	Weak transcription	Fetal Stomach	stomach
34	chr11:8934200-8935200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:8934200-8935200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:8934200-8935200	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:8934200-8935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr11:8934200-8935200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr11:8934200-8935400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:8934200-8935400	Weak transcription	Brain Germinal Matrix	brain
41	chr11:8934200-8935400	Enhancers	Fetal Brain Female	brain
42	chr11:8934200-8935600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr11:8934200-8935600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:8934200-8935600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:8934200-8935600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:8934200-8935600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr11:8934200-8935600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr11:8934200-8935600	Weak transcription	Fetal Brain Male	brain
49	chr11:8934200-8935600	Weak transcription	Ovary	ovary
50	chr11:8934200-8935600	Weak transcription	Rectal Mucosa Donor 29	rectum

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