Variant report

Variant	rs1205964
Chromosome Location	chr19:42724785-42724786
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	BACH1	chr19:42724215-42724937	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:42722971-42725156	PFSK-1	brain:	n/a	n/a
3	STAT5A	chr19:42724217-42724873	GM12878	blood:	n/a	chr19:42724846-42724855 chr19:42724845-42724854
4	NFYB	chr19:42724003-42724791	K562	blood:	n/a	chr19:42724413-42724428 chr19:42724414-42724428 chr19:42724441-42724455 chr19:42724438-42724453 chr19:42724415-42724428 chr19:42724413-42724428 chr19:42724415-42724430
5	MXI1	chr19:42724002-42724884	HepG2	liver:	n/a	n/a
6	MAX	chr19:42723900-42724910	SK-N-SH	brain:	n/a	chr19:42724316-42724326
7	POLR2A	chr19:42724072-42724819	A549	lung:	n/a	n/a
8	MYBL2	chr19:42724291-42724884	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:42723813-42725031	HUVEC	blood vessel:	n/a	n/a
10	TFAP2C	chr19:42724176-42725134	Hela-S3	cervix:	n/a	chr19:42724693-42724708
11	ELF1	chr19:42724131-42724859	GM12878	blood:	n/a	n/a
12	WRNIP1	chr19:42724118-42725086	GM12878	blood:	n/a	n/a
13	TAF1	chr19:42723782-42724932	PFSK-1	brain:	n/a	n/a
14	SP1	chr19:42723987-42724833	H1-hESC	embryonic stem cell:	n/a	chr19:42724406-42724427 chr19:42724315-42724327 chr19:42724316-42724325 chr19:42724587-42724601 chr19:42724316-42724326 chr19:42724442-42724463 chr19:42724316-42724326 chr19:42724315-42724327 chr19:42724317-42724326
15	MAX	chr19:42724080-42724890	MCF-7	breast:	n/a	chr19:42724316-42724326
16	MXI1	chr19:42723735-42725209	IMR90	lung:	n/a	n/a
17	POLR2A	chr19:42724032-42724822	GM19193	blood:	n/a	n/a
18	POLR2A	chr19:42724011-42724812	Hela-S3	cervix:	n/a	n/a
19	ELF1	chr19:42724187-42724891	GM12878	blood:	n/a	n/a
20	TAF1	chr19:42724035-42724876	ECC-1	luminal epithelium:	n/a	n/a
21	TBP	chr19:42723832-42724971	K562	blood:	n/a	n/a
22	POLR2A	chr19:42724009-42724846	ECC-1	luminal epithelium:	n/a	n/a
23	TAF1	chr19:42723945-42724884	K562	blood:	n/a	n/a
24	MXI1	chr19:42724117-42724839	GM12878	blood:	n/a	n/a
25	JUND	chr19:42724014-42724945	A549	lung:	n/a	chr19:42724415-42724424
26	RFX5	chr19:42723691-42724994	SK-N-SH	brain:	n/a	chr19:42724416-42724425
27	POLR2A	chr19:42723832-42724883	PBDE	blood:	n/a	n/a
28	REST	chr19:42723964-42725266	H1-neurons	neurons:	n/a	chr19:42724667-42724680 chr19:42724740-42724753 chr19:42724582-42724595 chr19:42725208-42725216
29	POLR2A	chr19:42724106-42724834	GM12878	blood:	n/a	n/a
30	MTA3	chr19:42724362-42724977	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:42724038-42724790	GM19099	blood:	n/a	n/a
32	ZBTB7A	chr19:42724244-42724815	K562	blood:	n/a	n/a
33	HEY1	chr19:42723913-42724812	K562	blood:	n/a	n/a
34	POLR2A	chr19:42724028-42724825	A549	lung:	n/a	n/a
35	E2F6	chr19:42724020-42724841	H1-hESC	embryonic stem cell:	n/a	chr19:42724291-42724300 chr19:42724806-42724820 chr19:42724379-42724388 chr19:42724185-42724197 chr19:42724809-42724816 chr19:42724809-42724816 chr19:42724417-42724426 chr19:42724809-42724816
36	IRF1	chr19:42723844-42725171	K562	blood:	n/a	chr19:42724566-42724575 chr19:42725071-42725085 chr19:42724313-42724327 chr19:42725073-42725087
37	TBP	chr19:42724082-42724832	HepG2	liver:	n/a	n/a
38	E2F4	chr19:42724412-42724928	GM12878	blood:	n/a	chr19:42724806-42724820 chr19:42724809-42724816 chr19:42724809-42724816 chr19:42724417-42724426 chr19:42724809-42724816
39	POLR2A	chr19:42724043-42725035	H1-hESC	embryonic stem cell:	n/a	n/a
40	ATF3	chr19:42723888-42724804	A549	lung:	n/a	chr19:42724659-42724668
41	POLR2A	chr19:42723775-42725021	IMR90	lung:	n/a	n/a
42	TAF1	chr19:42723888-42724806	K562	blood:	n/a	n/a
43	POLR2A	chr19:42724075-42724791	MCF-7	breast:	n/a	n/a
44	MAX	chr19:42723891-42724789	K562	blood:	n/a	chr19:42724316-42724326
45	HEY1	chr19:42723960-42724845	HepG2	liver:	n/a	n/a
46	MXI1	chr19:42723724-42725480	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr19:42724068-42724826	GM12878	blood:	n/a	n/a
48	ETS1	chr19:42724190-42724819	A549	lung:	n/a	n/a
49	POLR2A	chr19:42723973-42724787	HepG2	liver:	n/a	n/a
50	MYC	chr19:42723968-42724883	K562	blood:	n/a	chr19:42724316-42724326

No.	Distal block	Cell Line	Cell type
1	chr19:42721143..42723529-chr19:42724223..42726542,2	MCF-7	breast:
2	chr19:42722869..42725129-chr19:42828151..42831038,3	K562	blood:
3	chr19:42722916..42725353-chr19:42805921..42808141,2	K562	blood:
4	chr19:42724704..42726606-chr19:42754008..42756562,2	MCF-7	breast:
5	chr19:42720843..42724936-chr19:42805318..42808035,4	MCF-7	breast:
6	chr19:42722142..42727268-chr19:42743805..42748670,12	MCF-7	breast:
7	chr19:42719158..42725942-chr19:42744280..42751391,14	MCF-7	breast:
8	chr19:42724002..42724965-chr3:172468327..172468962,2	Hela-S3	cervix:

Variant related genes	Relation type
DEDD2	TF binding region
ENSG00000188368	Chromatin interaction
ENSG00000105429	Chromatin interaction
ENSG00000204957	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000114346	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000079462	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1055512	1.00[EUR][1000 genomes]
rs1152712	1.00[GIH][hapmap]
rs1685562	1.00[EUR][1000 genomes]
rs35272495	1.00[EUR][1000 genomes]
rs61733017	1.00[EUR][1000 genomes]
rs7254956	1.00[EUR][1000 genomes]
rs73552843	1.00[EUR][1000 genomes]
rs73552847	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs874013	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	nsv961292	chr19:42710814-42734591	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42720800-42725200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:42723600-42724800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:42723600-42725200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:42723600-42725200	Active TSS	Fetal Kidney	kidney
5	chr19:42723600-42725200	Active TSS	A549	lung
6	chr19:42723600-42725400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr19:42723600-42725800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:42723800-42724800	Active TSS	Placenta Amnion	Placenta Amnion
9	chr19:42723800-42725000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr19:42723800-42725000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr19:42723800-42725000	Active TSS	Left Ventricle	heart
12	chr19:42723800-42725200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:42723800-42725200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:42723800-42725200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr19:42723800-42725200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:42723800-42725200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:42723800-42725400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr19:42723800-42725400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr19:42723800-42725400	Active TSS	Aorta	Aorta
20	chr19:42723800-42725400	Active TSS	Psoas Muscle	Psoas
21	chr19:42723800-42725600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:42723800-42726000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:42724000-42724800	Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr19:42724000-42724800	Active TSS	Brain Hippocampus Middle	brain
25	chr19:42724000-42724800	Active TSS	Colon Smooth Muscle	Colon
26	chr19:42724000-42724800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr19:42724000-42724800	Active TSS	Thymus	Thymus
28	chr19:42724000-42725000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:42724000-42725000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:42724000-42725000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:42724000-42725000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:42724000-42725000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:42724000-42725000	Active TSS	Brain Angular Gyrus	brain
34	chr19:42724000-42725000	Active TSS	Esophagus	oesophagus
35	chr19:42724000-42725000	Active TSS	Fetal Heart	heart
36	chr19:42724000-42725000	Active TSS	Fetal Intestine Small	intestine
37	chr19:42724000-42725000	Active TSS	Fetal Stomach	stomach
38	chr19:42724000-42725000	Active TSS	Gastric	stomach
39	chr19:42724000-42725000	Active TSS	Ovary	ovary
40	chr19:42724000-42725000	Active TSS	Pancreas	Pancrea
41	chr19:42724000-42725000	Active TSS	Right Ventricle	heart
42	chr19:42724000-42725000	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr19:42724000-42725000	Active TSS	Small Intestine	intestine
44	chr19:42724000-42725000	Active TSS	Stomach Mucosa	stomach
45	chr19:42724000-42725000	Active TSS	Dnd41	blood
46	chr19:42724000-42725000	Active TSS	Hela-S3	cervix
47	chr19:42724000-42725200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:42724000-42725200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:42724000-42725200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:42724000-42725200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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