Variant report

Variant	rs4429390
Chromosome Location	chr19:44598868-44598869
allele	G/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	BCL3	chr19:44598022-44598915	A549	lung:	n/a	chr19:44598525-44598534
2	POLR2A	chr19:44598167-44598902	K562	blood:	n/a	n/a
3	SREBP1	chr19:44597634-44599876	GM12878	blood:	n/a	chr19:44599340-44599351
4	GABPA	chr19:44598133-44598919	MCF-7	breast:	n/a	n/a
5	GABPA	chr19:44597900-44599553	A549	lung:	n/a	n/a
6	ELF1	chr19:44598170-44598896	MCF-7	breast:	n/a	chr19:44598524-44598537
7	MAX	chr19:44598215-44598904	GM12878	blood:	n/a	chr19:44598788-44598799
8	GABPA	chr19:44597946-44599187	MCF-7	breast:	n/a	n/a
9	CTBP2	chr19:44598194-44598969	H1-hESC	embryonic stem cell:	n/a	n/a
10	BACH1	chr19:44598217-44599245	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr19:44598107-44599014	GM12878	blood:	n/a	n/a
12	KAP1	chr19:44597987-44598908	U2OS	brain:	n/a	n/a
13	POLR2A	chr19:44598150-44599104	GM18505	blood:	n/a	n/a
14	GABPA	chr19:44598276-44598875	HepG2	liver:	n/a	n/a
15	ELF1	chr19:44598172-44599362	GM12878	blood:	n/a	chr19:44599117-44599130 chr19:44599119-44599130 chr19:44598524-44598537 chr19:44599120-44599129
16	ZEB1	chr19:44598470-44598917	GM12878	blood:	n/a	chr19:44598789-44598796
17	MAX	chr19:44598193-44599019	K562	blood:	n/a	chr19:44598788-44598799
18	BRCA1	chr19:44598506-44598961	GM12878	blood:	n/a	n/a
19	MAX	chr19:44597979-44599342	A549	lung:	n/a	chr19:44598788-44598799
20	CHD2	chr19:44598213-44598889	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr19:44597950-44598895	U87	brain:	n/a	n/a
22	MAX	chr19:44598091-44599015	A549	lung:	n/a	chr19:44598788-44598799
23	POLR2A	chr19:44597987-44599054	HepG2	liver:	n/a	n/a
24	ELF1	chr19:44597993-44599019	HCT-116	colon:	n/a	chr19:44598524-44598537
25	POLR2A	chr19:44598103-44599014	PBDE	blood:	n/a	n/a
26	MYC	chr19:44598612-44598890	MCF-7	breast:	n/a	chr19:44598788-44598799
27	MAX	chr19:44598710-44598932	K562	blood:	n/a	chr19:44598788-44598799
28	SIN3AK20	chr19:44598043-44599742	MCF-7	breast:	n/a	n/a
29	POLR2A	chr19:44598197-44598981	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:44598169-44599319	GM19193	blood:	n/a	n/a
31	POLR2A	chr19:44598097-44599402	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:44597995-44598869	SK-N-MC	brain:	n/a	n/a
33	MAZ	chr19:44598110-44599114	K562	blood:	n/a	chr19:44598788-44598799
34	ELF1	chr19:44598111-44598951	HCT-116	colon:	n/a	chr19:44598524-44598537
35	SPI1	chr19:44598039-44598896	GM12878	blood:	n/a	n/a
36	PML	chr19:44598018-44599034	GM12878	blood:	n/a	n/a
37	MYC	chr19:44598180-44599052	K562	blood:	n/a	chr19:44598788-44598799
38	RUNX3	chr19:44598092-44599361	GM12878	blood:	n/a	n/a
39	MAX	chr19:44598226-44599200	Hela-S3	cervix:	n/a	chr19:44598788-44598799
40	REST	chr19:44598046-44599293	A549	lung:	n/a	n/a
41	TAF1	chr19:44597984-44599121	A549	lung:	n/a	n/a
42	POLR2A	chr19:44597878-44599021	PFSK-1	brain:	n/a	n/a
43	SIN3AK20	chr19:44598120-44598869	MCF-7	breast:	n/a	n/a
44	ELF1	chr19:44598181-44598904	K562	blood:	n/a	chr19:44598524-44598537
45	GABPA	chr19:44597930-44599058	A549	lung:	n/a	n/a
46	MTA3	chr19:44597991-44599365	GM12878	blood:	n/a	n/a
47	E2F6	chr19:44598755-44598925	K562	blood:	n/a	n/a
48	TCF12	chr19:44597966-44598987	A549	lung:	n/a	n/a
49	REST	chr19:44597957-44598887	H1-neurons	neurons:	n/a	n/a
50	EGR1	chr19:44598707-44598911	K562	blood:	n/a	chr19:44598822-44598835

No.	Distal block	Cell Line	Cell type
1	chr19:44596713..44600957-chr19:44644435..44647275,5	MCF-7	breast:
2	chr19:44555396..44557599-chr19:44598429..44600981,2	MCF-7	breast:
3	chr19:44506046..44508713-chr19:44597601..44599146,2	MCF-7	breast:
4	chr19:44589107..44593140-chr19:44596665..44599244,3	MCF-7	breast:
5	chr10:76586022..76586774-chr19:44598408..44598941,2	Hela-S3	cervix:
6	chr19:44555737..44557669-chr19:44596681..44600019,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF45-4	chr19:44598503-44599794	ENSG00000267163.1
2	lnc-ZNF284-1	chr19:44598543-44600094	NONHSAT066660

Variant related genes	Relation type
ZNF224	TF binding region
ENSG00000159882	Chromatin interaction
ENSG00000263002	Chromatin interaction
ENSG00000253021	Chromatin interaction
ENSG00000266921	Chromatin interaction
ENSG00000178386	Chromatin interaction
ENSG00000156650	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10406335	0.83[CHB][hapmap]
rs10408901	0.83[CHB][hapmap]
rs10410306	0.83[CHB][hapmap]
rs1236715	0.83[CHB][hapmap];0.88[TSI][hapmap]
rs1236716	0.83[CHB][hapmap];0.88[TSI][hapmap]
rs2061332	0.91[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs2061333	0.91[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs2068061	0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2284978	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2284980	0.83[CHB][hapmap]
rs2284981	0.83[CHB][hapmap]
rs3172	0.81[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs3746319	0.91[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs4239529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4459653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508518	0.87[CHB][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs4802204	0.86[EUR][1000 genomes]
rs4802205	0.86[EUR][1000 genomes]
rs4802206	0.82[CHB][hapmap]
rs4802207	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs4803676	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4803677	0.98[ASN][1000 genomes]
rs4803678	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4803679	0.98[ASN][1000 genomes]
rs4803680	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4803681	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs56353321	0.86[EUR][1000 genomes]
rs62115524	0.86[EUR][1000 genomes]
rs62115526	0.87[EUR][1000 genomes]
rs6509141	0.93[ASN][1000 genomes]
rs7249827	0.98[ASN][1000 genomes]
rs7249834	0.98[ASN][1000 genomes]
rs7250076	0.97[ASN][1000 genomes]
rs7250171	0.97[ASN][1000 genomes]
rs7508149	0.86[CHB][hapmap]
rs8099869	0.83[CHB][hapmap]
rs8101657	0.98[ASN][1000 genomes]
rs8104573	0.83[CHB][hapmap]
rs8105860	0.83[CHB][hapmap]
rs8108021	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs8113249	0.92[EUR][1000 genomes]
rs9304638	0.83[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4429390	SNORD34	cis	parietal	SCAN
rs4429390	NAPSB	cis	parietal	SCAN
rs4429390	APOE	cis	parietal	SCAN
rs4429390	SIGLEC12	cis	parietal	SCAN
rs4429390	TULP2	cis	cerebellum	SCAN
rs4429390	FUT2	cis	parietal	SCAN
rs4429390	RRAS	cis	cerebellum	SCAN
rs4429390	FPR2	cis	parietal	SCAN
rs4429390	CPT1C	cis	cerebellum	SCAN
rs4429390	KLK10	cis	cerebellum	SCAN
rs4429390	ZNF223	cis	Thyroid	GTEx
rs4429390	ZNF224	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44597800-44599400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:44597800-44599600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:44597800-44599800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:44597800-44599800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:44597800-44599800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:44597800-44599800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:44597800-44599800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:44597800-44599800	Active TSS	Primary hematopoietic stem cells	blood
9	chr19:44597800-44599800	Active TSS	Brain Anterior Caudate	brain
10	chr19:44597800-44599800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr19:44597800-44599800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr19:44597800-44599800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr19:44597800-44599800	Active TSS	HMEC	breast
14	chr19:44597800-44599800	Active TSS	K562	blood
15	chr19:44597800-44600000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:44597800-44600000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr19:44597800-44600000	Active TSS	Primary T cells from cord blood	blood
18	chr19:44597800-44600000	Active TSS	Stomach Smooth Muscle	stomach
19	chr19:44597800-44600000	Active TSS	A549	lung
20	chr19:44597800-44600200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:44598000-44599000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:44598000-44599000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:44598000-44599000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:44598000-44599200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:44598000-44599200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr19:44598000-44599200	Active TSS	Brain Hippocampus Middle	brain
27	chr19:44598000-44599200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr19:44598000-44599200	Active TSS	Fetal Brain Female	brain
29	chr19:44598000-44599200	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr19:44598000-44599400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:44598000-44599400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:44598000-44599400	Active TSS	Primary T cells fromperipheralblood	blood
33	chr19:44598000-44599400	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:44598000-44599400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:44598000-44599400	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr19:44598000-44599400	Active TSS	Fetal Brain Male	brain
37	chr19:44598000-44599400	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr19:44598000-44599400	Active TSS	Thymus	Thymus
39	chr19:44598000-44599600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:44598000-44599600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:44598000-44599600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr19:44598000-44599600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:44598000-44599600	Active TSS	Aorta	Aorta
44	chr19:44598000-44599600	Active TSS	Fetal Muscle Leg	muscle
45	chr19:44598000-44599600	Active TSS	Fetal Stomach	stomach
46	chr19:44598000-44599600	Active TSS	Fetal Thymus	thymus
47	chr19:44598000-44599600	Active TSS	Ovary	ovary
48	chr19:44598000-44599600	Active TSS	Pancreas	Pancrea
49	chr19:44598000-44599600	Active TSS	Placenta Amnion	Placenta Amnion
50	chr19:44598000-44599600	Active TSS	Stomach Mucosa	stomach

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