Variant report

Variant	rs390369
Chromosome Location	chr19:44506984-44506985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:389)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:389 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr19:44506790-44507229	K562	blood:	n/a	n/a
2	BHLHE40	chr19:44506745-44507917	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:44506762-44507632	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:44506629-44507354	MCF-7	breast:	n/a	n/a
5	GABPA	chr19:44506867-44507348	K562	blood:	n/a	chr19:44507267-44507276
6	POU2F2	chr19:44506799-44507753	GM12891	blood:	n/a	chr19:44507264-44507276
7	MYC	chr19:44506884-44507491	NB4	blood:	n/a	chr19:44507265-44507275
8	YY1	chr19:44506678-44507406	GM12878	blood:	n/a	chr19:44507267-44507276
9	TAF1	chr19:44506766-44507238	SK-N-SH	brain:	n/a	n/a
10	MAFK	chr19:44506861-44507238	HepG2	liver:	n/a	n/a
11	RCOR1	chr19:44506440-44507367	K562	blood:	n/a	n/a
12	SIN3AK20	chr19:44506761-44507315	A549	lung:	n/a	n/a
13	TAF1	chr19:44506687-44507297	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr19:44506673-44507443	ProgFib	skin:	n/a	n/a
15	CREB1	chr19:44506710-44507688	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:44506633-44507923	GM12878	blood:	n/a	n/a
17	ZNF143	chr19:44506729-44507350	H1-hESC	embryonic stem cell:	n/a	chr19:44506993-44507002 chr19:44506995-44507004 chr19:44507052-44507067 chr19:44507051-44507070 chr19:44507056-44507074
18	MAFK	chr19:44506772-44507261	HepG2	liver:	n/a	n/a
19	MYC	chr19:44506798-44507150	MCF10A-Er-Src	breast:	n/a	n/a
20	CHD2	chr19:44506775-44507654	GM12878	blood:	n/a	n/a
21	ZMIZ1	chr19:44506754-44507395	K562	blood:	n/a	n/a
22	YY1	chr19:44506791-44507216	GM12892	blood:	n/a	n/a
23	ELF1	chr19:44506751-44507449	MCF-7	breast:	n/a	chr19:44507099-44507110 chr19:44507099-44507110
24	SP1	chr19:44506647-44507414	A549	lung:	n/a	chr19:44507266-44507278 chr19:44507267-44507276 chr19:44507268-44507277 chr19:44507263-44507277 chr19:44507268-44507277
25	CEBPB	chr19:44506887-44507356	A549	lung:	n/a	n/a
26	POLR2A	chr19:44506381-44507453	MCF10A-Er-Src	breast:	n/a	n/a
27	YY1	chr19:44506751-44507373	ECC-1	luminal epithelium:	n/a	chr19:44507267-44507276
28	POLR2A	chr19:44506796-44507317	K562	blood:	n/a	n/a
29	PAX5	chr19:44506855-44507258	GM12878	blood:	n/a	chr19:44507099-44507108
30	USF2	chr19:44506920-44507273	Hela-S3	cervix:	n/a	n/a
31	SPI1	chr19:44506818-44507263	GM12891	blood:	n/a	n/a
32	CTCF	chr19:44506522-44507300	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:44506819-44507564	GM12891	blood:	n/a	n/a
34	POLR2A	chr19:44506762-44507370	H1-neurons	neurons:	n/a	n/a
35	NFIC	chr19:44506779-44507357	HepG2	liver:	n/a	n/a
36	TEAD4	chr19:44506756-44507234	H1-hESC	embryonic stem cell:	n/a	n/a
37	EP300	chr19:44506874-44507245	GM12878	blood:	n/a	chr19:44507100-44507107
38	CEBPB	chr19:44506959-44507245	HepG2	liver:	n/a	n/a
39	YY1	chr19:44506640-44507444	SK-N-SH	brain:	n/a	chr19:44507267-44507276
40	ELK1	chr19:44506792-44507264	K562	blood:	n/a	chr19:44507099-44507108 chr19:44507099-44507108
41	BCLAF1	chr19:44506694-44507591	GM12878	blood:	n/a	chr19:44507099-44507108
42	SIX5	chr19:44506792-44507165	H1-hESC	embryonic stem cell:	n/a	chr19:44506993-44507002 chr19:44506995-44507004
43	SIN3AK20	chr19:44506580-44507603	MCF-7	breast:	n/a	n/a
44	GABPA	chr19:44506410-44507830	A549	lung:	n/a	chr19:44507267-44507276
45	YY1	chr19:44506731-44507253	GM12891	blood:	n/a	n/a
46	MXI1	chr19:44506684-44507486	HepG2	liver:	n/a	n/a
47	CHD2	chr19:44506797-44507349	K562	blood:	n/a	n/a
48	MAX	chr19:44506738-44507410	GM12878	blood:	n/a	chr19:44507265-44507275
49	RELA	chr19:44506708-44507547	GM19099	blood:	n/a	n/a
50	POLR2A	chr19:44506474-44507683	PBDE	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:44506973-44507023	ProgFib	skin:	n/a
2	chr19:44506973-44507023	SAEC	small airway:	n/a
3	chr19:44506973-44507023	HCT-116	colon:	n/a
4	chr19:44506973-44507023	T-47D	breast:	n/a
5	chr19:44506973-44507023	SK-N-SH_RA	brain:	n/a
6	chr19:44506953-44507003	BJ	skin:	n/a
7	chr19:44506973-44507023	AG09309	skin:	n/a
8	chr19:44506953-44507003	LNCaP	prostate:	n/a
9	chr19:44506953-44507003	HCF	heart:	n/a
10	chr19:44506953-44507003	MCF-7	breast:	n/a
11	chr19:44506953-44507003	SAEC	small airway:	n/a
12	chr19:44506973-44507023	NH-A	brain:	n/a
13	chr19:44506953-44507003	AG09319	gingival:	n/a
14	chr19:44506953-44507003	Hepatocyte	liver:	n/a
15	chr19:44506973-44507023	SK-N-SH	brain:	n/a
16	chr19:44506953-44507003	ovcar-3	ovarian:	n/a
17	chr19:44506953-44507003	ProgFib	skin:	n/a
18	chr19:44506953-44507003	HAEpiC	amniotic membrane:	n/a
19	chr19:44506973-44507023	Caco-2	colon:	n/a
20	chr19:44506973-44507023	CMK	blood:	n/a
21	chr19:44506973-44507023	HRCEpiC	kidney:	n/a
22	chr19:44506953-44507003	PrEC	prostate:	n/a
23	chr19:44506953-44507003	GM12878	blood:	n/a
24	chr19:44506953-44507003	AG04450	lung:	fetal
25	chr19:44506953-44507003	HCT-116	colon:	n/a
26	chr19:44506953-44507003	PANC-1	pancreas:	n/a
27	chr19:44506953-44507003	IMR90	lung:	fetal
28	chr19:44506973-44507023	H1-hESC	embryonic stem cell:	embryo
29	chr19:44506953-44507003	NH-A	brain:	n/a
30	chr19:44506953-44507003	HNPCEpiC	eye:	n/a
31	chr19:44506973-44507023	HCM	heart:	n/a
32	chr19:44506973-44507023	Hepatocyte	liver:	n/a
33	chr19:44506973-44507023	SK-N-MC	brain:	n/a
34	chr19:44506973-44507023	PFSK-1	brain:	n/a
35	chr19:44506973-44507023	K562	blood:	n/a
36	chr19:44506953-44507003	HRE	kidney:	n/a
37	chr19:44506973-44507023	AG04449	skin:	fetal
38	chr19:44506953-44507003	HPAEpiC	pulmonary alveolar:	n/a
39	chr19:44506953-44507003	HepG2	liver:	n/a
40	chr19:44506973-44507023	GM12891	blood:	n/a
41	chr19:44506953-44507003	HL-60	blood:	n/a
42	chr19:44506953-44507003	AG04449	skin:	fetal
43	chr19:44506953-44507003	HRCEpiC	kidney:	n/a
44	chr19:44506973-44507023	IMR90	lung:	fetal
45	chr19:44506973-44507023	PrEC	prostate:	n/a
46	chr19:44506973-44507023	MCF-7	breast:	n/a
47	chr19:44506953-44507003	BE2_C	brain:	n/a
48	chr19:44506973-44507023	AG09319	gingival:	n/a
49	chr19:44506953-44507003	Caco-2	colon:	n/a
50	chr19:44506973-44507023	PANC-1	pancreas:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44486769..44491037-chr19:44505585..44508395,4	MCF-7	breast:
2	chr19:44506046..44508713-chr19:44597601..44599146,2	MCF-7	breast:
3	chr19:44506929..44508722-chr19:44508906..44512991,6	K562	blood:
4	chr19:44506934..44508722-chr19:44508906..44511281,4	K562	blood:
5	chr19:44506534..44508269-chr19:44616199..44620011,3	K562	blood:
6	chr19:44505664..44508645-chr19:44527908..44530282,2	MCF-7	breast:
7	chr19:44487658..44489792-chr19:44505545..44508358,4	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF45-2	chr19:44506776-44506988	ENSG00000266921.1
2	lnc-ZNF45-2	chr19:44506776-44506988	NONHSAT066650
3	lnc-ZNF45-2	chr19:44506417-44506985	ENSG00000266921.1

No data

Variant related genes	Relation type
ZNF230	TF binding region
ZNF230	CpG island
ENSG00000159882	Chromatin interaction
ENSG00000159885	Chromatin interaction
ENSG00000267144	Chromatin interaction
ENSG00000267022	Chromatin interaction
ENSG00000256294	Chromatin interaction
ENSG00000267680	Chromatin interaction
ENSG00000186019	Chromatin interaction
ENSG00000204920	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10418363	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083732	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083733	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11881151	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12232810	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996408	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2191566	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35292176	0.82[EUR][1000 genomes]
rs367209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377503	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810406	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs384544	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803667	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4803669	0.84[ASN][1000 genomes]
rs4803675	0.86[JPT][hapmap]
rs55703004	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101767	0.91[EUR][1000 genomes]
rs56171514	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56317065	0.82[ASN][1000 genomes]
rs59963278	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62115482	0.80[ASN][1000 genomes]
rs62119173	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62119176	0.87[ASN][1000 genomes]
rs6509133	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509138	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7245749	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252394	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253205	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254261	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7255145	0.91[ASN][1000 genomes]
rs7255315	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255512	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7256908	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258517	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs73037629	0.80[ASN][1000 genomes]
rs8104605	0.86[JPT][hapmap]
rs8105571	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs390369	HIF3A	cis	parietal	SCAN
rs390369	FOXA3	cis	cerebellum	SCAN
rs390369	ZNF155	cis	cerebellar cortex	BrainEAC
rs390369	ZNF155	cis	brain	BrainEAC
rs390369	OPA3	cis	cerebellum	SCAN
rs390369	OPA3	cis	parietal	SCAN
rs390369	CCDC114	cis	cerebellum	SCAN
rs390369	ZNF223	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44506000-44508400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:44506200-44507000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr19:44506200-44507000	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr19:44506200-44507200	Active TSS	Rectal Smooth Muscle	rectum
5	chr19:44506200-44507600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr19:44506200-44507600	Active TSS	Fetal Brain Female	brain
7	chr19:44506200-44507600	Active TSS	NH-A	brain
8	chr19:44506200-44507800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:44506200-44507800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:44506200-44507800	Active TSS	Right Atrium	heart
11	chr19:44506200-44507800	Active TSS	Stomach Mucosa	stomach
12	chr19:44506200-44508000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:44506200-44508000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:44506200-44508000	Active TSS	Psoas Muscle	Psoas
15	chr19:44506200-44508000	Active TSS	Right Ventricle	heart
16	chr19:44506200-44508000	Active TSS	HSMMtube	muscle
17	chr19:44506200-44508200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:44506200-44508200	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr19:44506200-44508200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr19:44506200-44508400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:44506200-44508400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:44506200-44508400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:44506200-44508400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr19:44506200-44508400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:44506200-44508400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:44506400-44507000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr19:44506400-44507000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr19:44506400-44507000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr19:44506400-44507000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr19:44506400-44507600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr19:44506400-44507600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:44506400-44507600	Active TSS	Colonic Mucosa	Colon
33	chr19:44506400-44507600	Active TSS	Fetal Muscle Leg	muscle
34	chr19:44506400-44507800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr19:44506400-44507800	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr19:44506400-44507800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:44506400-44507800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:44506400-44507800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:44506400-44508000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:44506400-44508000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:44506400-44508000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:44506400-44508000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:44506400-44508000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:44506400-44508000	Active TSS	Fetal Intestine Small	intestine
45	chr19:44506400-44508000	Active TSS	Left Ventricle	heart
46	chr19:44506400-44508000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr19:44506400-44508200	Active TSS	H1 Cell Line	embryonic stem cell
48	chr19:44506400-44508400	Active TSS	H9 Cell Line	embryonic stem cell
49	chr19:44506400-44508400	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr19:44506400-44508400	Active TSS	iPS-15b Cell Line	embryonic stem cell

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