Variant report

Variant	rs12980032
Chromosome Location	chr19:39283144-39283145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12461466	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461850	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980315	0.94[ASN][1000 genomes]
rs12981495	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12981542	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34465996	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34619818	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34960839	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58866020	0.94[ASN][1000 genomes]
rs62119011	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121412	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71356824	0.81[ASN][1000 genomes]
rs8110828	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv1064688	chr19:39249059-39291526	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv911671	chr19:39252238-39306425	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1063592	chr19:39257977-39287265	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv9720	chr19:39277331-39283376	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
11	nsv1058132	chr19:39279522-39302843	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv963045	chr19:39280546-39283148	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
13	nsv9721	chr19:39281857-39287128	Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39277200-39283200	Weak transcription	NH-A	brain
2	chr19:39279000-39283400	Weak transcription	HSMM	muscle
3	chr19:39279400-39283400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:39279600-39283200	Weak transcription	HepG2	liver
5	chr19:39279600-39283400	Weak transcription	A549	lung
6	chr19:39279800-39291600	Weak transcription	Stomach Mucosa	stomach
7	chr19:39281800-39283200	Active TSS	Duodenum Mucosa	Duodenum
8	chr19:39282200-39283200	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:39282200-39283200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:39282200-39291600	Weak transcription	Brain Anterior Caudate	brain
11	chr19:39282800-39283200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:39282800-39283200	Enhancers	HMEC	breast
13	chr19:39282800-39283400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:39282800-39283600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:39282800-39283600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr19:39282800-39283800	Enhancers	Primary B cells from cord blood	blood
17	chr19:39282800-39283800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:39282800-39284000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:39283000-39283200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:39283000-39283200	Enhancers	Primary T cells from cord blood	blood
21	chr19:39283000-39283200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr19:39283000-39283200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr19:39283000-39283200	Active TSS	Adipose Nuclei	Adipose
24	chr19:39283000-39283200	Enhancers	Brain Angular Gyrus	brain
25	chr19:39283000-39283200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr19:39283000-39283200	Enhancers	Brain Substantia Nigra	brain
27	chr19:39283000-39283200	Active TSS	Colonic Mucosa	Colon
28	chr19:39283000-39283200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
29	chr19:39283000-39283200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr19:39283000-39283200	Bivalent Enhancer	Fetal Stomach	stomach
31	chr19:39283000-39283200	Enhancers	NHEK	skin
32	chr19:39283000-39283400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:39283000-39283400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr19:39283000-39283400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr19:39283000-39283400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:39283000-39283400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr19:39283000-39283400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:39283000-39283400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:39283000-39283400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:39283000-39283400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:39283000-39283400	Enhancers	Liver	Liver
42	chr19:39283000-39283400	Active TSS	Brain Cingulate Gyrus	brain
43	chr19:39283000-39283400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
44	chr19:39283000-39283400	Active TSS	Left Ventricle	heart
45	chr19:39283000-39283400	Enhancers	Pancreas	Pancrea
46	chr19:39283000-39283400	Flanking Active TSS	Right Ventricle	heart
47	chr19:39283000-39283400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr19:39283000-39283600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr19:39283000-39283600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:39283000-39283600	Flanking Active TSS	Primary B cells from peripheral blood	blood

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