Variant report

Variant	rs12492290
Chromosome Location	chr3:113477350-113477351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10934239	0.87[AMR][1000 genomes]
rs10934240	0.87[AMR][1000 genomes]
rs11920913	0.87[AMR][1000 genomes]
rs12486414	1.00[AMR][1000 genomes]
rs12489192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490048	0.93[AMR][1000 genomes]
rs12490651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12491540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12492542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12492783	0.93[AMR][1000 genomes]
rs12493602	1.00[AMR][1000 genomes]
rs12493935	0.87[AMR][1000 genomes]
rs12494777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12495298	0.93[AMR][1000 genomes]
rs12495713	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12496604	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12496617	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12497754	1.00[AMR][1000 genomes]
rs16861230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861233	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861235	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861331	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2292512	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2566972	0.87[AMR][1000 genomes]
rs2603791	0.87[AMR][1000 genomes]
rs3773686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv482804	chr3:113432431-113581672	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv829678	chr3:113446177-113633053	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv877351	chr3:113450495-113637424	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1013746	chr3:113460162-113646657	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113466800-113489000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:113467200-113504000	Weak transcription	Fetal Stomach	stomach
3	chr3:113467200-113514800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:113467200-113528600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:113467600-113488400	Weak transcription	NH-A	brain
6	chr3:113467800-113477400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:113468000-113487800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:113468000-113488200	Weak transcription	A549	lung
9	chr3:113468000-113488600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:113468000-113495200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:113468000-113499800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:113468000-113502800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:113468200-113488400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:113468600-113488400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:113468800-113477400	Weak transcription	Liver	Liver
16	chr3:113469000-113477800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:113469000-113519400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:113469600-113502400	Weak transcription	Hela-S3	cervix
19	chr3:113469800-113499800	Weak transcription	Fetal Intestine Small	intestine
20	chr3:113472600-113505800	Weak transcription	Right Ventricle	heart
21	chr3:113472800-113504400	Weak transcription	Lung	lung
22	chr3:113473400-113483000	Weak transcription	Psoas Muscle	Psoas
23	chr3:113473400-113498800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:113473600-113477400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:113473600-113502400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:113473800-113492200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:113474200-113501600	Weak transcription	HUVEC	blood vessel
28	chr3:113474400-113477600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:113474400-113485800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:113475200-113478000	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr3:113476400-113480400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:113476600-113477800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:113476600-113488400	Weak transcription	HSMM	muscle
34	chr3:113477000-113478200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:113477200-113477400	ZNF genes & repeats	Dnd41	blood
36	chr3:113477200-113477600	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr3:113477200-113477800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr3:113477200-113477800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:113477200-113477800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:113477200-113477800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:113477200-113477800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:113477200-113477800	ZNF genes & repeats	Brain Substantia Nigra	brain
43	chr3:113477200-113477800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
44	chr3:113477200-113478000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr3:113477200-113478000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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