Variant report

Variant	rs73177909
Chromosome Location	chr3:119815768-119815769
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119811946-119816045	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:119811576-119817111	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:119815757-119815882	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:119815752-119815929	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:119811975-119815966	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr3:119815721-119816046	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:119815520-119816302	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119812158..119817554-chr3:119829250..119832588,6	K562	blood:
2	chr3:119181413..119183027-chr3:119814257..119816285,2	MCF-7	breast:
3	chr3:119815352..119817379-chr3:119819963..119822983,3	K562	blood:
4	chr3:119814526..119816268-chr3:119818029..119819760,2	K562	blood:
5	chr3:119812621..119817617-chr3:119824950..119830930,7	K562	blood:
6	chr3:119655041..119657977-chr3:119815420..119818415,2	K562	blood:
7	chr3:119812799..119816595-chr3:119829619..119835566,15	MCF-7	breast:
8	chr3:119408612..119410162-chr3:119814493..119816849,2	K562	blood:
9	chr3:119814026..119816300-chr3:120067212..120070079,2	MCF-7	breast:
10	chr3:119394727..119396286-chr3:119814089..119815777,2	K562	blood:
11	chr17:56708450..56710386-chr3:119813932..119815937,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1I2-1	chr3:119813266-119819259	NONHSAT091417

No data

Variant related genes	Relation type
GSK3B	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000244308	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000163428	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11925868	0.80[AFR][1000 genomes]
rs11925899	0.80[AFR][1000 genomes]
rs11925952	0.80[AFR][1000 genomes]
rs11927974	0.83[EUR][1000 genomes]
rs17811013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17811061	0.95[AFR][1000 genomes]
rs3755557	0.95[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119808000-119816400	Active TSS	Fetal Brain Female	brain
2	chr3:119809000-119816200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:119809200-119815800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:119809200-119816000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:119809200-119816200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:119809400-119815800	Active TSS	HSMM	muscle
7	chr3:119809400-119816000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr3:119809600-119815800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:119809600-119815800	Active TSS	NHLF	lung
10	chr3:119809600-119816000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr3:119809800-119815800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:119809800-119815800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr3:119810000-119815800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:119810000-119816200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:119810000-119816200	Active TSS	K562	blood
16	chr3:119810200-119816000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr3:119810200-119816400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr3:119814600-119830600	Weak transcription	Gastric	stomach
19	chr3:119814800-119815800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:119814800-119815800	Flanking Active TSS	NHEK	skin
21	chr3:119814800-119816000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr3:119814800-119816000	Enhancers	Spleen	Spleen
23	chr3:119815000-119816000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:119815000-119816000	Flanking Active TSS	Dnd41	blood
25	chr3:119815000-119818000	Enhancers	Small Intestine	intestine
26	chr3:119815000-119829200	Weak transcription	Ovary	ovary
27	chr3:119815200-119815800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:119815200-119815800	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:119815200-119815800	Enhancers	Brain Substantia Nigra	brain
30	chr3:119815200-119815800	Weak transcription	Pancreas	Pancrea
31	chr3:119815200-119816000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:119815200-119816000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr3:119815200-119816000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:119815200-119816000	Enhancers	Left Ventricle	heart
35	chr3:119815200-119816000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr3:119815200-119816200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr3:119815200-119816400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:119815200-119816400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr3:119815200-119816400	Enhancers	Stomach Mucosa	stomach
40	chr3:119815200-119817000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:119815200-119817600	Enhancers	Placenta	Placenta
42	chr3:119815200-119819000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:119815200-119822000	Weak transcription	Esophagus	oesophagus
44	chr3:119815400-119815800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:119815400-119815800	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr3:119815400-119815800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:119815400-119815800	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr3:119815400-119815800	Active TSS	Hela-S3	cervix
49	chr3:119815400-119816000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:119815400-119816000	Enhancers	Primary hematopoietic stem cells	blood

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