Variant report

Variant	rs7973613
Chromosome Location	chr12:1553450-1553451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11061763	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300475	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309872	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318883	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319342	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16927897	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928432	1.00[CEU][hapmap]
rs16928470	1.00[MEX][hapmap]
rs16928476	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs16928479	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16928481	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16928482	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17800906	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2057801	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55888927	0.97[EUR][1000 genomes]
rs58023561	1.00[ASN][1000 genomes]
rs59053653	0.90[EUR][1000 genomes]
rs59394469	1.00[ASN][1000 genomes]
rs59624680	0.97[EUR][1000 genomes]
rs6489287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73597964	0.82[EUR][1000 genomes]
rs73597965	0.82[EUR][1000 genomes]
rs7969825	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2762958	chr12:1049279-1554962	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1052559	chr12:1077964-1588543	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1046134	chr12:1153489-1675223	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv541344	chr12:1153489-1675223	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
11	nsv556944	chr12:1308553-1569097	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv1054178	chr12:1372157-1682699	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS 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 target site	14 gene(s)	inside rSNPs	diseases
13	nsv541347	chr12:1372157-1682699	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv1035935	chr12:1400974-1608625	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv1044918	chr12:1432740-1584649	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv541348	chr12:1432740-1584649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	nsv1046515	chr12:1440896-1588543	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
18	nsv1039488	chr12:1486636-1567275	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
19	esv3397478	chr12:1535455-1730159	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1527600-1554600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:1530800-1554600	Weak transcription	Spleen	Spleen
3	chr12:1530800-1554600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:1530800-1583000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:1531400-1554600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:1531400-1554800	Weak transcription	Primary B cells from cord blood	blood
7	chr12:1531400-1574200	Weak transcription	Thymus	Thymus
8	chr12:1532200-1555200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:1532400-1554400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:1532400-1581000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:1532600-1554600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:1532600-1557200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:1538200-1554800	Weak transcription	Adipose Nuclei	Adipose
14	chr12:1538200-1557200	Weak transcription	Brain Angular Gyrus	brain
15	chr12:1539200-1554400	Weak transcription	Brain Anterior Caudate	brain
16	chr12:1541800-1553800	Weak transcription	NHEK	skin
17	chr12:1544000-1554400	Weak transcription	Placenta	Placenta
18	chr12:1544000-1554600	Weak transcription	Lung	lung
19	chr12:1544800-1582800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:1545000-1554800	Weak transcription	Liver	Liver
21	chr12:1545000-1559600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:1545000-1583000	Weak transcription	HepG2	liver
23	chr12:1545200-1557800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:1545400-1553800	Weak transcription	Fetal Intestine Small	intestine
25	chr12:1545400-1554400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:1545400-1554600	Weak transcription	Stomach Mucosa	stomach
27	chr12:1545400-1557800	Weak transcription	Pancreas	Pancrea
28	chr12:1545400-1566000	Weak transcription	Gastric	stomach
29	chr12:1545400-1570600	Weak transcription	Fetal Intestine Large	intestine
30	chr12:1546000-1554600	Weak transcription	Right Ventricle	heart
31	chr12:1546000-1564200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:1546000-1582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:1546600-1554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:1546600-1557400	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:1546600-1583200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:1546800-1558800	Weak transcription	Brain Substantia Nigra	brain
37	chr12:1548600-1554800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:1548600-1559400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:1549000-1557200	Weak transcription	Fetal Lung	lung
40	chr12:1550400-1559800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:1551200-1554600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:1551200-1554800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:1552000-1555600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr12:1552200-1554600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:1552200-1560400	Weak transcription	Brain Germinal Matrix	brain
46	chr12:1552400-1553600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:1552400-1553600	Enhancers	HSMMtube	muscle
48	chr12:1552400-1554800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:1552400-1559600	Weak transcription	Fetal Thymus	thymus
50	chr12:1552600-1553600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links