Variant report

Variant	rs55888927
Chromosome Location	chr12:1573748-1573749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1572175..1574157-chr12:1679717..1682384,2	K562	blood:
2	chr12:1569039..1571648-chr12:1571859..1575051,3	K562	blood:
3	chr12:1570379..1574393-chr12:1574873..1580232,6	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11061763	0.97[EUR][1000 genomes]
rs12300475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12306978	0.81[EUR][1000 genomes]
rs12309872	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12318883	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12319342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12319376	0.97[EUR][1000 genomes]
rs16927897	0.97[EUR][1000 genomes]
rs16928476	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928479	1.00[ASN][1000 genomes]
rs17800906	0.80[EUR][1000 genomes]
rs2057801	0.90[EUR][1000 genomes]
rs59053653	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59624680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489287	0.97[EUR][1000 genomes]
rs73597964	0.80[EUR][1000 genomes]
rs73597965	0.80[EUR][1000 genomes]
rs7973613	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1049247	chr12:1566534-1671806	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv1002676	chr12:1570806-1578110	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:88 , 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	chr12:1546000-1582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:1546600-1583200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:1552600-1582600	Weak transcription	A549	lung
9	chr12:1552800-1598000	Weak transcription	Esophagus	oesophagus
10	chr12:1553400-1582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:1553600-1581800	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:1554000-1582600	Weak transcription	Ovary	ovary
13	chr12:1554200-1582600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:1554800-1574800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:1555200-1584200	Weak transcription	Spleen	Spleen
16	chr12:1555400-1582600	Weak transcription	Placenta	Placenta
17	chr12:1555400-1582600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:1555800-1581600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:1556200-1583000	Weak transcription	Hela-S3	cervix
20	chr12:1557600-1581800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:1558000-1582400	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:1558000-1583000	Weak transcription	Brain Angular Gyrus	brain
23	chr12:1558200-1574400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:1558200-1582000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:1558400-1574400	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:1558400-1599400	Weak transcription	Pancreas	Pancrea
27	chr12:1558600-1581400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:1558800-1574200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:1558800-1574600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:1558800-1574800	Weak transcription	Fetal Stomach	stomach
31	chr12:1559800-1582600	Weak transcription	Primary B cells from cord blood	blood
32	chr12:1560800-1575600	Weak transcription	Fetal Intestine Small	intestine
33	chr12:1562600-1574800	Weak transcription	Lung	lung
34	chr12:1563400-1582800	Weak transcription	Brain Anterior Caudate	brain
35	chr12:1563800-1574600	Weak transcription	Liver	Liver
36	chr12:1563800-1574800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:1566400-1578200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:1566600-1581400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:1566600-1581600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr12:1566600-1581800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:1567400-1574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:1567400-1578200	Weak transcription	Right Ventricle	heart
43	chr12:1567400-1581000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:1567400-1599600	Weak transcription	Gastric	stomach
45	chr12:1568200-1574200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:1568200-1578000	Weak transcription	HSMMtube	muscle
47	chr12:1569000-1578000	Weak transcription	HSMM	muscle
48	chr12:1571600-1580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr12:1571800-1575600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:1571800-1577800	Weak transcription	NHDF-Ad	bronchial

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