Variant report

Variant	rs1859390
Chromosome Location	chr12:1525353-1525354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16928413	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs757477	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7953630	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	42 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv898581	chr12:1084783-1527359	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	nsv1050361	chr12:1274052-1541558	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	nsv1039946	chr12:1429190-1548852	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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
22	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1859390	SLC30A8	trans	lymphoblastoid	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1486800-1530400	Weak transcription	Fetal Lung	lung
2	chr12:1492400-1531200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:1498400-1529800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:1500800-1527200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:1500800-1528800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:1501000-1529800	Weak transcription	Gastric	stomach
7	chr12:1501200-1530400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:1501200-1544400	Weak transcription	Right Ventricle	heart
9	chr12:1501400-1530400	Weak transcription	Brain Substantia Nigra	brain
10	chr12:1501400-1530400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:1501600-1529800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:1501600-1530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:1501800-1530400	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:1504000-1528000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:1505400-1530400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:1506400-1530400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:1508400-1538000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:1511800-1530400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:1512800-1530200	Weak transcription	Fetal Heart	heart
20	chr12:1514000-1530200	Weak transcription	A549	lung
21	chr12:1515200-1530400	Weak transcription	Aorta	Aorta
22	chr12:1515400-1529600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:1515400-1529800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:1515600-1530000	Weak transcription	Fetal Brain Female	brain
25	chr12:1515800-1529800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:1516200-1530400	Weak transcription	Fetal Kidney	kidney
27	chr12:1516400-1529600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:1516400-1530400	Weak transcription	HMEC	breast
29	chr12:1516400-1537600	Weak transcription	NHDF-Ad	bronchial
30	chr12:1516600-1526000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:1516800-1526200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:1516800-1529800	Weak transcription	Spleen	Spleen
33	chr12:1517000-1528800	Weak transcription	Psoas Muscle	Psoas
34	chr12:1517200-1525800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:1517200-1526000	Strong transcription	Primary T cells from cord blood	blood
36	chr12:1517200-1526200	Weak transcription	HepG2	liver
37	chr12:1517200-1529600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:1517400-1525600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:1518400-1526200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:1518400-1534200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:1518600-1525800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:1518600-1527400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:1518600-1530400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:1518600-1537600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:1518600-1553400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:1518800-1529800	Weak transcription	HSMM	muscle
47	chr12:1518800-1530400	Weak transcription	Brain Anterior Caudate	brain
48	chr12:1518800-1530400	Weak transcription	HSMMtube	muscle
49	chr12:1519800-1530200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:1520800-1525800	Weak transcription	Hela-S3	cervix

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