Variant report

Variant	rs11123145
Chromosome Location	chr2:113406691-113406692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113406506-113406908	A549	lung:	n/a	n/a
2	POLR2A	chr2:113403115-113407903	K562	blood:	n/a	n/a
3	POLR2A	chr2:113406286-113406986	K562	blood:	n/a	n/a
4	POLR2A	chr2:113401765-113425023	U87	brain:	n/a	n/a
5	POLR2A	chr2:113406543-113406765	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:113401707-113407973	U87	brain:	n/a	n/a
7	POLR2A	chr2:113406248-113406822	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:113401928-113406954	HCT-116	colon:	n/a	n/a
9	POLR2A	chr2:113402016-113412293	Hela-S3	cervix:	n/a	n/a
10	EBF1	chr2:113406601-113406769	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:113406461-113407621	PFSK-1	brain:	n/a	n/a
12	FOXA1	chr2:113406675-113407007	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:113406527-113406975	K562	blood:	n/a	n/a
14	POLR2A	chr2:113404419-113407819	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:113406565-113406865	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:113406360-113406962	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:113401943-113419910	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr2:113404319-113407079	K562	blood:	n/a	n/a
19	FOXA1	chr2:113406633-113407018	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:113401765-113425014	U87	brain:	n/a	n/a
21	POLR2A	chr2:113406521-113406986	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:113401719-113411441	U87	brain:	n/a	n/a
23	POLR2A	chr2:113406341-113406923	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:113406445-113407016	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:113406226-113407078	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
2	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
3	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
4	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
5	chr2:113374574..113376775-chr2:113406157..113408747,2	K562	blood:

No data

Variant related genes	Relation type
SLC20A1	TF binding region
ENSG00000237753	TF binding region
ENSG00000125611	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1061254	0.84[AFR][1000 genomes]
rs11123144	0.84[AFR][1000 genomes]
rs13023311	0.85[AFR][1000 genomes]
rs1516791	0.83[AFR][1000 genomes]
rs2312699	0.91[AFR][1000 genomes]
rs4630766	0.90[AFR][1000 genomes]
rs4848286	0.90[AFR][1000 genomes]
rs4849090	0.82[AFR][1000 genomes]
rs4849092	0.87[AFR][1000 genomes]
rs4849093	0.90[AFR][1000 genomes]
rs4849094	0.90[AFR][1000 genomes]
rs4849095	0.89[AFR][1000 genomes]
rs4849096	0.90[AFR][1000 genomes]
rs4849100	0.89[AFR][1000 genomes]
rs6737094	0.82[AFR][1000 genomes]
rs6751117	0.91[AFR][1000 genomes]
rs6793	0.90[AFR][1000 genomes]
rs885346	0.91[AFR][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	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11123145	AC079922.3	cis	lung	GTEx
rs11123145	AC079922.3	cis	Nerve Tibial	GTEx
rs11123145	FLJ42351	cis	brain	BrainEAC
rs11123145	AC079922.3	cis	Heart Left Ventricle	GTEx
rs11123145	AC079922.3	cis	Artery Aorta	GTEx
rs11123145	AC079922.3	cis	Whole Blood	GTEx
rs11123145	AC079922.3	cis	Esophagus Muscularis	GTEx
rs11123145	AC079922.3	cis	Stomach	GTEx
rs11123145	AC079922.3	cis	Esophagus Mucosa	GTEx
rs11123145	AC079922.3	cis	Thyroid	GTEx
rs11123145	AC079922.3	cis	Muscle Skeletal	GTEx
rs11123145	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs11123145	AC079922.3	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113403600-113407200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:113404000-113407600	Transcr. at gene 5' and 3'	NHEK	skin
3	chr2:113404000-113409000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
4	chr2:113404000-113409600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:113404400-113406800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:113404400-113406800	Transcr. at gene 5' and 3'	HSMMtube	muscle
7	chr2:113404400-113407000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:113404400-113407000	Transcr. at gene 5' and 3'	HSMM	muscle
9	chr2:113404400-113407200	Transcr. at gene 5' and 3'	NHLF	lung
10	chr2:113404400-113407400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
11	chr2:113404400-113407400	Transcr. at gene 5' and 3'	K562	blood
12	chr2:113404400-113407600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:113404400-113407600	Transcr. at gene 5' and 3'	Osteobl	bone
14	chr2:113404400-113407800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr2:113404400-113407800	Transcr. at gene 5' and 3'	HMEC	breast
20	chr2:113404400-113407800	Transcr. at gene 5' and 3'	NH-A	brain
21	chr2:113404400-113410600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:113404600-113407200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
23	chr2:113404600-113407800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:113404600-113407800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
25	chr2:113404600-113409800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:113404800-113407000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
27	chr2:113404800-113407400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
28	chr2:113404800-113407400	Transcr. at gene 5' and 3'	Hela-S3	cervix
29	chr2:113404800-113412600	Weak transcription	Gastric	stomach
30	chr2:113404800-113414400	Weak transcription	Esophagus	oesophagus
31	chr2:113404800-113416200	Weak transcription	Ovary	ovary
32	chr2:113404800-113416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:113405000-113407000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:113405000-113407000	Genic enhancers	Adipose Nuclei	Adipose
35	chr2:113405000-113407000	Genic enhancers	Brain Anterior Caudate	brain
36	chr2:113405000-113407200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:113405000-113407400	Genic enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:113405000-113408000	Weak transcription	Lung	lung
39	chr2:113405000-113409400	Weak transcription	Spleen	Spleen
40	chr2:113405000-113411200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:113405000-113413200	Strong transcription	Placenta	Placenta
42	chr2:113405000-113416200	Weak transcription	Aorta	Aorta
43	chr2:113405000-113416400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:113405000-113423200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:113405200-113407000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:113405200-113407000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:113405200-113407600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:113405200-113407600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr2:113405200-113407800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:113405200-113407800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood

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