Variant report

Variant	rs12075450
Chromosome Location	chr1:180085620-180085621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10798729	0.80[JPT][hapmap]
rs10913916	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs10913917	0.81[JPT][hapmap]
rs10913918	0.84[CEU][hapmap]
rs10913927	0.93[JPT][hapmap]
rs12091685	0.81[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12094391	0.83[EUR][1000 genomes]
rs16855164	0.84[ASN][1000 genomes]
rs1981314	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2319676	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2319677	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs2319773	0.92[ASN][1000 genomes]
rs2477106	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs2477111	0.81[JPT][hapmap]
rs2477112	0.81[JPT][hapmap]
rs2477115	0.84[EUR][1000 genomes]
rs2477117	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs2477118	0.81[JPT][hapmap]
rs2477119	0.86[JPT][hapmap]
rs2483622	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs2501608	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs2501611	0.81[JPT][hapmap]
rs2501613	0.81[JPT][hapmap]
rs2501614	0.89[EUR][1000 genomes]
rs2501615	0.81[JPT][hapmap]
rs2501618	0.82[EUR][1000 genomes]
rs2501621	0.80[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs2762859	0.81[JPT][hapmap]
rs3767201	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs3818999	0.81[JPT][hapmap]
rs3930305	0.93[JPT][hapmap]
rs4076449	0.93[JPT][hapmap]
rs4147170	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs4256775	0.93[JPT][hapmap]
rs4263962	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4379644	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4622030	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs4651055	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4652461	0.84[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4652464	0.92[ASN][1000 genomes]
rs4652465	0.93[JPT][hapmap]
rs483307	0.81[JPT][hapmap]
rs510209	0.81[JPT][hapmap]
rs552743	0.84[CEU][hapmap]
rs55953436	0.91[EUR][1000 genomes]
rs55971224	0.90[EUR][1000 genomes]
rs6425602	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6425603	0.93[JPT][hapmap]
rs6425606	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs6425607	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs6657347	0.93[JPT][hapmap]
rs6659911	0.85[ASN][1000 genomes]
rs6660984	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6676989	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682558	0.88[CEU][hapmap]
rs6692394	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7412536	0.80[ASN][1000 genomes]
rs7521948	0.81[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544467	0.88[ASN][1000 genomes]
rs7547954	0.84[EUR][1000 genomes]
rs9286932	0.93[JPT][hapmap]
rs9425849	0.93[JPT][hapmap]
rs9425852	0.84[ASN][1000 genomes]
rs9425853	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9425854	0.93[JPT][hapmap]
rs9425857	0.88[ASN][1000 genomes]
rs9425858	0.91[ASN][1000 genomes]
rs9425859	0.80[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9425861	0.93[JPT][hapmap]
rs9887843	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180052800-180085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:180080000-180087000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:180080600-180086200	Weak transcription	Esophagus	oesophagus
4	chr1:180080600-180086400	Weak transcription	Stomach Mucosa	stomach
5	chr1:180080600-180090400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:180080600-180091000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:180080800-180086000	Weak transcription	Right Ventricle	heart
8	chr1:180080800-180086800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:180081000-180086000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:180081200-180085800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:180081200-180086000	Weak transcription	Spleen	Spleen
12	chr1:180081200-180086200	Weak transcription	Aorta	Aorta
13	chr1:180081200-180086200	Weak transcription	Colonic Mucosa	Colon
14	chr1:180081200-180086200	Weak transcription	Gastric	stomach
15	chr1:180081200-180088600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:180081200-180089800	Weak transcription	Fetal Brain Female	brain
17	chr1:180081800-180086000	Weak transcription	Lung	lung
18	chr1:180081800-180086200	Weak transcription	NHDF-Ad	bronchial
19	chr1:180081800-180086400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:180081800-180086400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:180082000-180086200	Weak transcription	A549	lung
22	chr1:180082000-180086400	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:180082000-180092400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:180082200-180085800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:180082200-180085800	Weak transcription	Fetal Kidney	kidney
26	chr1:180082200-180086000	Weak transcription	Hela-S3	cervix
27	chr1:180082200-180086200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:180082200-180086200	Weak transcription	Placenta	Placenta
29	chr1:180082200-180086400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:180082200-180086400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:180082200-180086400	Weak transcription	Fetal Intestine Large	intestine
32	chr1:180082200-180086400	Weak transcription	NH-A	brain
33	chr1:180082200-180086400	Weak transcription	Osteobl	bone
34	chr1:180082200-180086600	Weak transcription	Psoas Muscle	Psoas
35	chr1:180082200-180086800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:180082200-180087600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:180082400-180085800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:180082400-180085800	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:180082400-180085800	Weak transcription	GM12878-XiMat	blood
40	chr1:180082400-180085800	Weak transcription	K562	blood
41	chr1:180082400-180086000	Weak transcription	Primary B cells from cord blood	blood
42	chr1:180082400-180086000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:180082400-180086200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:180082400-180086200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:180082400-180086400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:180082400-180086400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:180082600-180085800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:180082600-180086600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:180082600-180087400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:180082600-180087400	Weak transcription	Fetal Thymus	thymus

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