Variant report

Variant	rs72971030
Chromosome Location	chr3:119816780-119816781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119811576-119817111	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:119816703-119816872	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:119816731-119817080	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:119812158..119817554-chr3:119829250..119832588,6	K562	blood:
2	chr3:119815352..119817379-chr3:119819963..119822983,3	K562	blood:
3	chr3:119812621..119817617-chr3:119824950..119830930,7	K562	blood:
4	chr3:119816323..119819155-chr3:119879849..119882520,2	MCF-7	breast:
5	chr3:119655041..119657977-chr3:119815420..119818415,2	K562	blood:
6	chr3:119816356..119819205-chr3:119850914..119853051,2	MCF-7	breast:
7	chr3:119408612..119410162-chr3:119814493..119816849,2	K562	blood:
8	chr3:119647743..119650107-chr3:119815940..119817594,2	MCF-7	breast:
9	chr3:119776406..119778250-chr3:119816051..119818083,2	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
ENSG00000244308	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs57147159	1.00[AMR][1000 genomes]
rs60282320	1.00[AMR][1000 genomes]
rs72952818	1.00[AMR][1000 genomes]
rs72952850	1.00[AMR][1000 genomes]
rs72952852	1.00[AMR][1000 genomes]
rs72952863	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952877	1.00[AMR][1000 genomes]
rs72952884	1.00[AMR][1000 genomes]
rs72954705	1.00[AMR][1000 genomes]
rs72954727	1.00[AMR][1000 genomes]
rs72954733	1.00[AMR][1000 genomes]
rs72954750	1.00[AMR][1000 genomes]
rs72954753	1.00[AMR][1000 genomes]
rs72954777	1.00[AMR][1000 genomes]
rs72954784	1.00[AMR][1000 genomes]
rs72967200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72971057	0.84[AFR][1000 genomes];1.00[AMR][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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119814600-119830600	Weak transcription	Gastric	stomach
2	chr3:119815000-119818000	Enhancers	Small Intestine	intestine
3	chr3:119815000-119829200	Weak transcription	Ovary	ovary
4	chr3:119815200-119817000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:119815200-119817600	Enhancers	Placenta	Placenta
6	chr3:119815200-119819000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:119815200-119822000	Weak transcription	Esophagus	oesophagus
8	chr3:119815400-119817200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:119815400-119817200	Weak transcription	Fetal Intestine Small	intestine
10	chr3:119815400-119817600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:119815400-119817600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:119815400-119817800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:119815400-119818400	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:119815400-119819600	Weak transcription	Primary T cells from cord blood	blood
15	chr3:119815400-119819600	Weak transcription	HSMMtube	muscle
16	chr3:119815400-119821000	Weak transcription	Adipose Nuclei	Adipose
17	chr3:119815400-119821000	Weak transcription	NH-A	brain
18	chr3:119815400-119821600	Weak transcription	Psoas Muscle	Psoas
19	chr3:119815400-119828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:119815400-119828200	Weak transcription	Aorta	Aorta
21	chr3:119815400-119828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:119815400-119830000	Weak transcription	Fetal Lung	lung
23	chr3:119815600-119817600	Weak transcription	NHDF-Ad	bronchial
24	chr3:119815600-119820600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:119815600-119821200	Weak transcription	Fetal Kidney	kidney
26	chr3:119815600-119826000	Weak transcription	Primary B cells from cord blood	blood
27	chr3:119815800-119816800	Weak transcription	HSMM	muscle
28	chr3:119815800-119819400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:119815800-119819400	Weak transcription	NHLF	lung
30	chr3:119815800-119829000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:119816000-119816800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:119816000-119817000	Enhancers	Dnd41	blood
33	chr3:119816000-119817200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:119816000-119817200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:119816000-119817200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:119816000-119817200	Weak transcription	Fetal Intestine Large	intestine
37	chr3:119816000-119817400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:119816000-119817400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:119816000-119817800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:119816000-119817800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:119816000-119818400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:119816000-119818400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:119816000-119819800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:119816000-119819800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:119816000-119820200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:119816000-119821000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:119816000-119821000	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:119816000-119821200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:119816000-119821600	Weak transcription	Fetal Stomach	stomach
50	chr3:119816000-119821600	Weak transcription	Left Ventricle	heart

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