Variant report

Variant	rs34270590
Chromosome Location	chr19:39657858-39657859
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	USF1	chr19:39657672-39657914	HepG2	liver:	n/a	chr19:39657802-39657813
2	NFIC	chr19:39657598-39658693	ECC-1	luminal epithelium:	n/a	n/a
3	MYC	chr19:39657785-39658011	MCF-7	breast:	n/a	chr19:39657862-39657872
4	TCF12	chr19:39657224-39658735	ECC-1	luminal epithelium:	n/a	chr19:39657746-39657753 chr19:39657653-39657663 chr19:39658413-39658423 chr19:39658216-39658226 chr19:39657699-39657706
5	NFIC	chr19:39657721-39658097	HepG2	liver:	n/a	n/a
6	NFIC	chr19:39657543-39658664	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr19:39657760-39657910	SK-N-SH_RA	brain:	n/a	n/a
8	GATA3	chr19:39657485-39658774	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr19:39657004-39658769	MCF-7	breast:	n/a	n/a
10	TCF12	chr19:39657639-39658724	ECC-1	luminal epithelium:	n/a	chr19:39657746-39657753 chr19:39657653-39657663 chr19:39658413-39658423 chr19:39658216-39658226 chr19:39657699-39657706
11	USF1	chr19:39657697-39657900	H1-hESC	embryonic stem cell:	n/a	chr19:39657802-39657813
12	TCF12	chr19:39657094-39658802	MCF-7	breast:	n/a	chr19:39657746-39657753 chr19:39657653-39657663 chr19:39658413-39658423 chr19:39658216-39658226 chr19:39657699-39657706
13	MYC	chr19:39657771-39658005	MCF-7	breast:	n/a	chr19:39657862-39657872
14	POLR2A	chr19:39657819-39658009	HepG2	liver:	n/a	n/a
15	HDAC2	chr19:39657119-39658732	MCF-7	breast:	n/a	n/a
16	MXI1	chr19:39657119-39658563	SK-N-SH	brain:	n/a	n/a
17	USF1	chr19:39657674-39657951	SK-N-SH_RA	brain:	n/a	chr19:39657802-39657813
18	MAX	chr19:39657566-39658663	MCF-7	breast:	n/a	chr19:39658325-39658335 chr19:39657862-39657872
19	ZBTB7A	chr19:39657244-39658643	ECC-1	luminal epithelium:	n/a	chr19:39658314-39658322
20	SIN3AK20	chr19:39657066-39658655	MCF-7	breast:	n/a	n/a
21	NR2F2	chr19:39657035-39658984	MCF-7	breast:	n/a	n/a
22	NR2F2	chr19:39657305-39658707	MCF-7	breast:	n/a	n/a
23	HDAC2	chr19:39657199-39658620	MCF-7	breast:	n/a	n/a
24	MAZ	chr19:39657814-39658097	HepG2	liver:	n/a	chr19:39657862-39657872
25	ZBTB7A	chr19:39657718-39657899	HepG2	liver:	n/a	n/a
26	MXI1	chr19:39657740-39657939	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:39657801-39658756	MCF-7	breast:	n/a	n/a
28	ZNF263	chr19:39657752-39658164	HEK293-T-REx	kidney:	n/a	chr19:39657931-39657952
29	POLR2A	chr19:39657672-39658187	MCF-7	breast:	n/a	n/a
30	POLR2A	chr19:39657808-39658021	K562	blood:	n/a	n/a
31	GATA3	chr19:39657113-39658609	MCF-7	breast:	n/a	n/a
32	ZNF217	chr19:39657802-39658543	MCF-7	breast:	n/a	n/a
33	ZBTB7A	chr19:39657350-39658665	ECC-1	luminal epithelium:	n/a	chr19:39658314-39658322
34	MAX	chr19:39657100-39658751	MCF-7	breast:	n/a	chr19:39658325-39658335 chr19:39657862-39657872
35	POLR2A	chr19:39657595-39658444	ECC-1	luminal epithelium:	n/a	n/a
36	USF1	chr19:39657671-39658009	SK-N-SH_RA	brain:	n/a	chr19:39657802-39657813
37	USF1	chr19:39657631-39657954	H1-hESC	embryonic stem cell:	n/a	chr19:39657802-39657813
38	POLR2A	chr19:39653429-39659123	K562	blood:	n/a	n/a
39	MAX	chr19:39657842-39657891	HepG2	liver:	n/a	chr19:39657862-39657872
40	USF1	chr19:39657625-39658034	ECC-1	luminal epithelium:	n/a	chr19:39657802-39657813

No.	Distal block	Cell Line	Cell type
1	chr19:39656337..39658753-chr19:39667505..39669573,2	MCF-7	breast:
2	chr19:39657697..39659384-chr19:39897167..39900031,2	MCF-7	breast:
3	chr19:39572549..39576644-chr19:39655893..39659798,4	MCF-7	breast:
4	chr19:39614796..39618723-chr19:39655193..39659848,7	MCF-7	breast:
5	chr19:39657376..39659366-chr19:39880631..39883470,2	MCF-7	breast:

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000183760	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000006712	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1079442	0.84[EUR][1000 genomes]
rs11083509	0.83[EUR][1000 genomes]
rs11083510	0.82[EUR][1000 genomes]
rs12610624	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12611361	0.83[EUR][1000 genomes]
rs12611365	0.84[EUR][1000 genomes]
rs12611376	0.83[EUR][1000 genomes]
rs12984418	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17722300	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17795295	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2873913	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34058542	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34110379	0.82[EUR][1000 genomes]
rs34326918	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34808880	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34846983	0.81[EUR][1000 genomes]
rs35163943	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35591784	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36148214	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3889485	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55748546	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61171111	0.81[EUR][1000 genomes]
rs67248178	0.84[EUR][1000 genomes]
rs71356839	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71356840	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71356841	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs737450	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8107629	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
4	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
5	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
8	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:39645200-39659000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:39645800-39658000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:39646600-39659000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:39646800-39659200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:39646800-39660600	Weak transcription	Dnd41	blood
14	chr19:39647200-39660400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:39647600-39660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:39647600-39664800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:39647800-39670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:39649200-39659400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:39649400-39659400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:39649600-39659400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr19:39649800-39659800	Weak transcription	Primary T cells from cord blood	blood
22	chr19:39651200-39659000	Weak transcription	Thymus	Thymus
23	chr19:39651800-39660600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr19:39651800-39660800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr19:39652000-39658400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:39652000-39659600	Weak transcription	NHLF	lung
27	chr19:39652000-39660400	Weak transcription	Adipose Nuclei	Adipose
28	chr19:39652000-39660600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:39652000-39660800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:39652200-39661000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:39652400-39660000	Weak transcription	Osteobl	bone
32	chr19:39652400-39661000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:39652600-39660600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:39653400-39658400	Enhancers	Spleen	Spleen
35	chr19:39653800-39663200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:39654000-39658600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:39654000-39660000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:39654000-39660600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:39654000-39661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:39654200-39658400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:39654200-39674000	Weak transcription	K562	blood
42	chr19:39655200-39659400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:39655400-39658000	Enhancers	Liver	Liver
44	chr19:39656000-39659000	Enhancers	Pancreas	Pancrea
45	chr19:39656200-39658200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr19:39656200-39658200	Enhancers	Placenta	Placenta
47	chr19:39656400-39658000	Enhancers	Brain Substantia Nigra	brain
48	chr19:39656400-39658200	Enhancers	Brain Cingulate Gyrus	brain
49	chr19:39656400-39658200	Enhancers	Stomach Smooth Muscle	stomach
50	chr19:39656400-39658400	Enhancers	Brain Hippocampus Middle	brain

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