Variant report

Variant	rs1516791
Chromosome Location	chr2:113405853-113405854
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:113405708-113406283	K562	blood:	n/a	n/a
2	POLR2A	chr2:113405115-113406117	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr2:113403115-113407903	K562	blood:	n/a	n/a
4	MXI1	chr2:113401955-113406269	SK-N-SH	brain:	n/a	chr2:113403307-113403316 chr2:113403983-113403992
5	POLR2A	chr2:113401765-113425023	U87	brain:	n/a	n/a
6	YY1	chr2:113405638-113405979	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr2:113401707-113407973	U87	brain:	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	POLR2A	chr2:113405752-113406117	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr2:113404419-113407819	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:113401943-113419910	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr2:113405592-113405977	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr2:113404319-113407079	K562	blood:	n/a	n/a
15	CHD1	chr2:113401468-113406380	IMR90	lung:	n/a	chr2:113404360-113404367
16	POLR2A	chr2:113401765-113425014	U87	brain:	n/a	n/a
17	POLR2A	chr2:113401719-113411441	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
2	chr2:113401688..113406035-chr2:113480430..113485744,11	MCF-7	breast:
3	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
4	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
5	chr2:113400575..113405879-chr2:113475243..113481233,15	K562	blood:
6	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
7	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
8	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
9	chr2:113339547..113342143-chr2:113401632..113406213,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000237753	TF binding region
SLC20A1	TF binding region
ENSG00000231747	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11123145	0.83[AFR][1000 genomes]
rs2312699	0.84[AFR][1000 genomes]
rs4630766	0.82[AFR][1000 genomes]
rs4848286	0.83[AFR][1000 genomes]
rs4849093	0.83[AFR][1000 genomes]
rs4849094	0.83[AFR][1000 genomes]
rs4849095	0.82[AFR][1000 genomes]
rs4849096	0.82[AFR][1000 genomes]
rs4849100	0.82[AFR][1000 genomes]
rs6751117	0.84[AFR][1000 genomes]
rs6793	0.82[AFR][1000 genomes]
rs885346	0.84[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1516791	AC079922.3	cis	lung	GTEx
rs1516791	AC079922.3	cis	Esophagus Muscularis	GTEx
rs1516791	AC079922.3	cis	Artery Tibial	GTEx
rs1516791	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs1516791	AC079922.3	cis	Thyroid	GTEx
rs1516791	AC079922.3	cis	Nerve Tibial	GTEx
rs1516791	AC079922.3	cis	Muscle Skeletal	GTEx
rs1516791	AC079922.3	cis	Heart Left Ventricle	GTEx
rs1516791	AC079922.3	cis	Esophagus Mucosa	GTEx
rs1516791	AC079922.3	cis	Artery Aorta	GTEx
rs1516791	AC079922.3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113403600-113406200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:113403600-113407200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:113403800-113406200	Flanking Active TSS	Thymus	Thymus
4	chr2:113404000-113407600	Transcr. at gene 5' and 3'	NHEK	skin
5	chr2:113404000-113409000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
6	chr2:113404000-113409600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:113404400-113406000	Transcr. at gene 5' and 3'	A549	lung
8	chr2:113404400-113406200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:113404400-113406400	Transcr. at gene 5' and 3'	HepG2	liver
10	chr2:113404400-113406800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:113404400-113406800	Transcr. at gene 5' and 3'	HSMMtube	muscle
12	chr2:113404400-113407000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:113404400-113407000	Transcr. at gene 5' and 3'	HSMM	muscle
14	chr2:113404400-113407200	Transcr. at gene 5' and 3'	NHLF	lung
15	chr2:113404400-113407400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
16	chr2:113404400-113407400	Transcr. at gene 5' and 3'	K562	blood
17	chr2:113404400-113407600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:113404400-113407600	Transcr. at gene 5' and 3'	Osteobl	bone
19	chr2:113404400-113407800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:113404400-113407800	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr2:113404400-113407800	Transcr. at gene 5' and 3'	HMEC	breast
25	chr2:113404400-113407800	Transcr. at gene 5' and 3'	NH-A	brain
26	chr2:113404400-113410600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:113404600-113406200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
28	chr2:113404600-113406400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
29	chr2:113404600-113406600	Enhancers	Small Intestine	intestine
30	chr2:113404600-113407200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
31	chr2:113404600-113407800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:113404600-113407800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
33	chr2:113404600-113409800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:113404800-113406000	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr2:113404800-113406200	Enhancers	Fetal Heart	heart
36	chr2:113404800-113406400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
37	chr2:113404800-113406400	Active TSS	Right Ventricle	heart
38	chr2:113404800-113406600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:113404800-113406600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:113404800-113406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:113404800-113407000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
42	chr2:113404800-113407400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
43	chr2:113404800-113407400	Transcr. at gene 5' and 3'	Hela-S3	cervix
44	chr2:113404800-113412600	Weak transcription	Gastric	stomach
45	chr2:113404800-113414400	Weak transcription	Esophagus	oesophagus
46	chr2:113404800-113416200	Weak transcription	Ovary	ovary
47	chr2:113404800-113416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:113405000-113406000	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
49	chr2:113405000-113406000	Genic enhancers	Fetal Lung	lung
50	chr2:113405000-113406000	Weak transcription	Stomach Smooth Muscle	stomach

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