Variant report

Variant	rs10592
Chromosome Location	chr3:179114471-179114472
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	GATA3	chr3:179114290-179114490	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr3:179113778-179116835	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNB4-1	chr3:179113877-179115965	ENSG00000269728.1

Variant related genes	Relation type
ENSG00000242539	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13313931	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13327891	1.00[EUR][1000 genomes]
rs28642912	1.00[EUR][1000 genomes]
rs3853150	1.00[EUR][1000 genomes]
rs3853151	1.00[EUR][1000 genomes]
rs3853152	1.00[EUR][1000 genomes]
rs6779649	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6780301	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6791769	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6795513	0.87[AMR][1000 genomes]
rs6808409	0.87[AMR][1000 genomes]
rs73045195	1.00[EUR][1000 genomes]
rs7355960	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7356002	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809536	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9816934	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820636	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821850	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869905	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9874433	1.00[EUR][1000 genomes]
rs9883260	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179066400-179136600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:179066800-179118800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:179067200-179131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:179070600-179120000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
6	chr3:179081600-179115200	Weak transcription	Spleen	Spleen
7	chr3:179081600-179120400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
9	chr3:179087200-179122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:179087600-179120000	Weak transcription	Right Ventricle	heart
11	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:179088600-179115400	Weak transcription	Aorta	Aorta
13	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
15	chr3:179098400-179120200	Weak transcription	Lung	lung
16	chr3:179098400-179125000	Weak transcription	Ovary	ovary
17	chr3:179099400-179119400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:179099600-179119600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:179101600-179125800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:179101800-179115800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:179101800-179119200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:179101800-179125800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:179102200-179126400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:179103200-179120600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:179103400-179114600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:179103400-179115600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:179103400-179115600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:179103400-179115800	Strong transcription	Adipose Nuclei	Adipose
30	chr3:179103400-179115800	Strong transcription	Fetal Thymus	thymus
31	chr3:179103400-179116200	Strong transcription	HSMM	muscle
32	chr3:179103400-179116400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:179103400-179119000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:179103600-179120200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:179103800-179116400	Strong transcription	Primary T cells from cord blood	blood
36	chr3:179105000-179131200	Weak transcription	Fetal Heart	heart
37	chr3:179105200-179115400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:179105400-179141400	Weak transcription	Thymus	Thymus
40	chr3:179105600-179115200	Weak transcription	Pancreas	Pancrea
41	chr3:179106800-179117000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:179106800-179119000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:179107000-179115600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:179107000-179116800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:179108000-179116000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:179108200-179115600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:179108400-179123400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:179108600-179116000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:179108600-179116600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr3:179109400-179117600	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links