Variant report

Variant	rs12309872
Chromosome Location	chr12:1565454-1565455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11061763	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300475	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306978	0.81[EUR][1000 genomes]
rs12318883	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319342	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319376	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16927897	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928432	1.00[CEU][hapmap]
rs16928476	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16928479	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16928481	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16928482	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17800906	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2057801	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55888927	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58023561	1.00[ASN][1000 genomes]
rs59053653	0.88[EUR][1000 genomes]
rs59394469	1.00[ASN][1000 genomes]
rs59624680	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6489287	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73597964	0.80[EUR][1000 genomes]
rs73597965	0.80[EUR][1000 genomes]
rs7969825	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7973613	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv573	chr12:1560167-1604539	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1530800-1583000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:1531400-1574200	Weak transcription	Thymus	Thymus
3	chr12:1532400-1581000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:1544800-1582800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:1545000-1583000	Weak transcription	HepG2	liver
6	chr12:1545400-1566000	Weak transcription	Gastric	stomach
7	chr12:1545400-1570600	Weak transcription	Fetal Intestine Large	intestine
8	chr12:1546000-1582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:1546600-1583200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:1552600-1582600	Weak transcription	A549	lung
11	chr12:1552800-1572200	Weak transcription	Fetal Brain Female	brain
12	chr12:1552800-1598000	Weak transcription	Esophagus	oesophagus
13	chr12:1553000-1566000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:1553000-1567000	Weak transcription	Psoas Muscle	Psoas
15	chr12:1553200-1565800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:1553400-1572800	Weak transcription	Fetal Kidney	kidney
17	chr12:1553400-1582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:1553600-1567000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:1553600-1568200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:1553600-1572400	Weak transcription	Right Atrium	heart
21	chr12:1553600-1581800	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:1553800-1567000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:1554000-1566000	Weak transcription	HSMM	muscle
24	chr12:1554000-1566800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:1554000-1582600	Weak transcription	Ovary	ovary
26	chr12:1554200-1572200	Weak transcription	Aorta	Aorta
27	chr12:1554200-1582600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:1554400-1566800	Weak transcription	NHEK	skin
29	chr12:1554600-1567000	Weak transcription	HMEC	breast
30	chr12:1554800-1574800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:1555200-1566600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:1555200-1566800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:1555200-1584200	Weak transcription	Spleen	Spleen
34	chr12:1555400-1566400	Weak transcription	Osteobl	bone
35	chr12:1555400-1567200	Weak transcription	Right Ventricle	heart
36	chr12:1555400-1582600	Weak transcription	Placenta	Placenta
37	chr12:1555400-1582600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:1555600-1566400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:1555800-1581600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:1556000-1572400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:1556200-1583000	Weak transcription	Hela-S3	cervix
42	chr12:1557000-1566800	Strong transcription	Primary T cells from cord blood	blood
43	chr12:1557600-1581800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:1557800-1566800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:1558000-1566400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:1558000-1566800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:1558000-1567000	Weak transcription	NHLF	lung
48	chr12:1558000-1582400	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:1558000-1583000	Weak transcription	Brain Angular Gyrus	brain
50	chr12:1558200-1565800	Weak transcription	Fetal Muscle Trunk	muscle

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