Variant report

Variant	rs12973448
Chromosome Location	chr19:39895110-39895111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr19:39891779-39895197	GM12878	blood:	n/a	chr19:39893578-39893594
2	SIX5	chr19:39891566-39895143	A549	lung:	n/a	chr19:39894997-39895011
3	MTA3	chr19:39891387-39895114	GM12878	blood:	n/a	n/a
4	SP1	chr19:39891503-39895118	A549	lung:	n/a	chr19:39894608-39894620 chr19:39894269-39894283 chr19:39893924-39893935 chr19:39893420-39893432 chr19:39893416-39893430 chr19:39894609-39894623 chr19:39894414-39894423 chr19:39894610-39894619 chr19:39893475-39893482 chr19:39894478-39894492 chr19:39893421-39893435 chr19:39893889-39893900 chr19:39893422-39893431 chr19:39894608-39894620 chr19:39894609-39894618 chr19:39894603-39894613 chr19:39893855-39893866 chr19:39893417-39893426
5	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:39891669-39895138	GM12892	blood:	n/a	n/a
7	MAX	chr19:39891523-39895116	A549	lung:	n/a	chr19:39894254-39894263 chr19:39894736-39894746 chr19:39893071-39893087
8	SIN3AK20	chr19:39893971-39895117	A549	lung:	n/a	n/a
9	E2F6	chr19:39893979-39895117	A549	lung:	n/a	n/a
10	PML	chr19:39894181-39895115	GM12878	blood:	n/a	chr19:39894550-39894558 chr19:39894252-39894261
11	POLR2A	chr19:39891652-39895381	IMR90	lung:	n/a	n/a
12	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr19:39891445-39895265	GM12878	blood:	n/a	n/a
14	TCF12	chr19:39891369-39895203	A549	lung:	n/a	chr19:39893338-39893348
15	POLR2A	chr19:39891621-39895119	GM12892	blood:	n/a	n/a
16	JUND	chr19:39893856-39895123	SK-N-SH	brain:	n/a	chr19:39894624-39894634 chr19:39894254-39894262 chr19:39894621-39894632 chr19:39894735-39894744 chr19:39894254-39894262 chr19:39894254-39894261 chr19:39894252-39894264 chr19:39894253-39894263
17	SIN3AK20	chr19:39891072-39895487	PANC-1	pancreas:	n/a	n/a
18	EP300	chr19:39893843-39895114	A549	lung:	n/a	chr19:39894254-39894263
19	POLR2A	chr19:39891677-39895135	GM12878	blood:	n/a	n/a
20	GATA3	chr19:39893862-39895158	A549	lung:	n/a	chr19:39894623-39894632
21	MAZ	chr19:39891567-39895110	IMR90	lung:	n/a	chr19:39894254-39894263 chr19:39894736-39894746 chr19:39893071-39893087
22	SP1	chr19:39891927-39895125	HCT-116	colon:	n/a	chr19:39894608-39894620 chr19:39894269-39894283 chr19:39893924-39893935 chr19:39893420-39893432 chr19:39893416-39893430 chr19:39894609-39894623 chr19:39894414-39894423 chr19:39894610-39894619 chr19:39893475-39893482 chr19:39894478-39894492 chr19:39893421-39893435 chr19:39893889-39893900 chr19:39893422-39893431 chr19:39894608-39894620 chr19:39894609-39894618 chr19:39894603-39894613 chr19:39893855-39893866 chr19:39893417-39893426
23	SP1	chr19:39893834-39895123	HCT-116	colon:	n/a	chr19:39894608-39894620 chr19:39894269-39894283 chr19:39893924-39893935 chr19:39894609-39894623 chr19:39894414-39894423 chr19:39894610-39894619 chr19:39894478-39894492 chr19:39893889-39893900 chr19:39894608-39894620 chr19:39894609-39894618 chr19:39894603-39894613 chr19:39893855-39893866
24	POLR2A	chr19:39891507-39895323	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39615977..39618241-chr19:39893024..39896089,3	MCF-7	breast:
2	chr19:39893196..39895716-chr19:39934783..39936652,2	MCF-7	breast:

Variant related genes	Relation type
ZFP36	TF binding region
ENSG00000130669	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10402122	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10403504	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10412877	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414216	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10423565	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425594	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11665856	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11672863	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12977767	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251864	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3843755	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803235	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs565545	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7250966	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7253005	0.93[EUR][1000 genomes]
rs7256692	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[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	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
9	esv3318773	chr19:39890112-39895210	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	esv3318775	chr19:39890112-39895210	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv911686	chr19:39891219-39907781	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
12	nsv911687	chr19:39891219-39909714	Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
13	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39891600-39895200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr19:39891800-39895200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:39891800-39895200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr19:39892400-39895200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:39892800-39895200	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr19:39893000-39895200	Flanking Active TSS	Fetal Intestine Large	intestine
7	chr19:39893200-39895200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr19:39893200-39895400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:39893200-39896800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:39893200-39897000	Weak transcription	Gastric	stomach
11	chr19:39893400-39895200	Active TSS	Right Ventricle	heart
12	chr19:39893800-39895200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:39893800-39896200	Weak transcription	Dnd41	blood
14	chr19:39894000-39895200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr19:39894200-39895400	Weak transcription	Spleen	Spleen
16	chr19:39894200-39896600	Weak transcription	HepG2	liver
17	chr19:39894200-39897000	Weak transcription	Ovary	ovary
18	chr19:39894200-39897000	Weak transcription	Pancreas	Pancrea
19	chr19:39894400-39895200	Enhancers	Placenta	Placenta
20	chr19:39894400-39896800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:39894400-39896800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:39894600-39895200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr19:39894600-39895200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:39894600-39896600	Enhancers	NHDF-Ad	bronchial
25	chr19:39894800-39895200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:39894800-39895200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr19:39894800-39895200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr19:39894800-39895200	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr19:39894800-39895200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr19:39894800-39895200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:39894800-39895200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:39894800-39895200	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr19:39894800-39895200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr19:39894800-39895200	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr19:39894800-39895200	Flanking Active TSS	Hela-S3	cervix
36	chr19:39894800-39895800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:39894800-39896400	Enhancers	Fetal Thymus	thymus
38	chr19:39894800-39896800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:39894800-39896800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr19:39894800-39897000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:39894800-39897200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr19:39894800-39897200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr19:39895000-39895200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:39895000-39895200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr19:39895000-39895200	Enhancers	Colon Smooth Muscle	Colon
46	chr19:39895000-39895200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr19:39895000-39895200	Enhancers	Fetal Stomach	stomach
48	chr19:39895000-39895200	Enhancers	Left Ventricle	heart
49	chr19:39895000-39895200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr19:39895000-39895200	Weak transcription	Small Intestine	intestine

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