Variant report

Variant	rs324094
Chromosome Location	chr19:52956753-52956754
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	GABPA	chr19:52956411-52957232	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr19:52956500-52956976	ECC-1	luminal epithelium:	n/a	n/a
3	GATA2	chr19:52956362-52957062	SH-SY5Y	brain:	n/a	n/a
4	ELF1	chr19:52956552-52957021	GM12878	blood:	n/a	chr19:52956818-52956827 chr19:52956767-52956778 chr19:52956765-52956778 chr19:52956767-52956778 chr19:52956817-52956828 chr19:52956768-52956777
5	POLR2A	chr19:52956553-52957083	HL-60	blood:	n/a	n/a
6	TAF1	chr19:52956742-52956917	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr19:52956636-52957081	SK-N-SH	brain:	n/a	n/a
8	ELF1	chr19:52956508-52957128	SK-N-SH	brain:	n/a	chr19:52956818-52956827 chr19:52956767-52956778 chr19:52956765-52956778 chr19:52956767-52956778 chr19:52956817-52956828 chr19:52956768-52956777
9	MAX	chr19:52956587-52957018	SK-N-SH	brain:	n/a	n/a
10	CHD2	chr19:52956662-52957034	H1-hESC	embryonic stem cell:	n/a	n/a
11	GABPA	chr19:52956517-52957024	K562	blood:	n/a	n/a
12	ZBTB33	chr19:52956649-52956956	SK-N-SH	brain:	n/a	n/a
13	HCFC1	chr19:52956706-52956825	K562	blood:	n/a	n/a
14	GABPA	chr19:52956706-52956885	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:52956729-52956954	H1-hESC	embryonic stem cell:	n/a	n/a
16	ELF1	chr19:52956602-52957048	SK-N-SH	brain:	n/a	chr19:52956818-52956827 chr19:52956767-52956778 chr19:52956765-52956778 chr19:52956767-52956778 chr19:52956817-52956828 chr19:52956768-52956777
17	CTCF	chr19:52956620-52956770	HMF	breast:	n/a	n/a
18	MAX	chr19:52956533-52957008	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr19:52956696-52956985	H1-neurons	neurons:	n/a	n/a
20	GABPA	chr19:52956416-52957220	SK-N-SH	brain:	n/a	n/a
21	EP300	chr19:52956592-52957060	ECC-1	luminal epithelium:	n/a	chr19:52956770-52956777
22	GABPA	chr19:52956439-52957188	HL-60	blood:	n/a	n/a
23	ZBTB33	chr19:52956648-52957022	SK-N-SH	brain:	n/a	n/a
24	MXI1	chr19:52956236-52957611	SK-N-SH	brain:	n/a	n/a
25	CHD2	chr19:52956737-52956809	K562	blood:	n/a	n/a
26	MAX	chr19:52956523-52957016	SK-N-SH	brain:	n/a	n/a
27	GABPA	chr19:52956311-52957309	HL-60	blood:	n/a	n/a
28	MAZ	chr19:52956691-52956837	K562	blood:	n/a	n/a
29	ELF1	chr19:52956533-52956949	K562	blood:	n/a	chr19:52956818-52956827 chr19:52956767-52956778 chr19:52956765-52956778 chr19:52956767-52956778 chr19:52956817-52956828 chr19:52956768-52956777
30	GABPA	chr19:52956708-52956883	GM12878	blood:	n/a	n/a
31	GABPA	chr19:52956689-52956949	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr19:52956563-52957068	ECC-1	luminal epithelium:	n/a	n/a
33	GABPA	chr19:52956566-52957017	K562	blood:	n/a	n/a
34	POLR2A	chr19:52956704-52956943	SK-N-SH	brain:	n/a	n/a
35	BRCA1	chr19:52956684-52956878	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr19:52956716-52956909	H1-hESC	embryonic stem cell:	n/a	n/a
37	ELF1	chr19:52956634-52956964	K562	blood:	n/a	chr19:52956818-52956827 chr19:52956767-52956778 chr19:52956765-52956778 chr19:52956767-52956778 chr19:52956817-52956828 chr19:52956768-52956777
38	CTCF	chr19:52956620-52956770	NHDF-neo	bronchial:	n/a	n/a
39	POLR2A	chr19:52956610-52956979	K562	blood:	n/a	n/a
40	NRF1	chr19:52956539-52957358	SK-N-SH	brain:	n/a	n/a
41	SIN3AK20	chr19:52956654-52956977	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52956729-52956779	NHBE	bronchial:	n/a
2	chr19:52956729-52956779	HEEpiC	esophagus:	n/a
3	chr19:52956729-52956779	HMEC	breast:	n/a
4	chr19:52956729-52956779	HCF	heart:	n/a
5	chr19:52956729-52956779	PFSK-1	brain:	n/a
6	chr19:52956729-52956779	SAEC	small airway:	n/a
7	chr19:52956729-52956779	AG04449	skin:	fetal
8	chr19:52956729-52956779	NT2-D1	testis:	n/a
9	chr19:52956729-52956779	HUVEC	blood vessel:	n/a
10	chr19:52956729-52956779	MCF-7	breast:	n/a
11	chr19:52956729-52956779	ECC-1	luminal epithelium:	n/a
12	chr19:52956729-52956779	LNCaP	prostate:	n/a
13	chr19:52956729-52956779	A549	lung:	n/a
14	chr19:52956729-52956779	AG04450	lung:	fetal
15	chr19:52956729-52956779	HRE	kidney:	n/a
16	chr19:52956729-52956779	GM12892	blood:	n/a
17	chr19:52956729-52956779	BE2_C	brain:	n/a
18	chr19:52956729-52956779	HRPEpiC	eye:	n/a
19	chr19:52956729-52956779	HIPEpiC	eye:	n/a
20	chr19:52956729-52956779	HEK293	kidney:	embryo
21	chr19:52956729-52956779	NH-A	brain:	n/a
22	chr19:52956729-52956779	HAEpiC	amniotic membrane:	n/a
23	chr19:52956729-52956779	ovcar-3	ovarian:	n/a
24	chr19:52956729-52956779	ProgFib	skin:	n/a
25	chr19:52956729-52956779	GM19239	blood:	n/a
26	chr19:52956729-52956779	Hela-S3	cervix:	n/a
27	chr19:52956729-52956779	Jurkat	blood:	n/a
28	chr19:52956729-52956779	Caco-2	colon:	n/a
29	chr19:52956729-52956779	PANC-1	pancreas:	n/a
30	chr19:52956729-52956779	MCF10A-Er-Src	breast:	n/a
31	chr19:52956729-52956779	HCPEpiC	choroid plexus:	n/a
32	chr19:52956729-52956779	U87	brain:	n/a
33	chr19:52956729-52956779	GM06990	blood:	n/a
34	chr19:52956729-52956779	AG09309	skin:	n/a
35	chr19:52956729-52956779	AG10803	skin:	n/a
36	chr19:52956729-52956779	SK-N-MC	brain:	n/a
37	chr19:52956729-52956779	AoSMC	blood vessel:	n/a
38	chr19:52956729-52956779	HCT-116	colon:	n/a
39	chr19:52956729-52956779	HPAEpiC	pulmonary alveolar:	n/a
40	chr19:52956729-52956779	RPTEC	kidney:	n/a
41	chr19:52956729-52956779	GM12891	blood:	n/a
42	chr19:52956729-52956779	HL-60	blood:	n/a
43	chr19:52956729-52956779	AG09319	gingival:	n/a
44	chr19:52956729-52956779	SK-N-SH	brain:	n/a
45	chr19:52956729-52956779	CMK	blood:	n/a
46	chr19:52956729-52956779	IMR90	lung:	fetal
47	chr19:52956729-52956779	SK-N-SH_RA	brain:	n/a
48	chr19:52956729-52956779	BJ	skin:	n/a
49	chr19:52956729-52956779	H1-hESC	embryonic stem cell:	embryo
50	chr19:52956729-52956779	K562	blood:	n/a

Variant related genes	Relation type
ZNF578	TF binding region
ZNF578	CpG island

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1112889	0.87[AFR][1000 genomes]
rs1115659	0.88[AFR][1000 genomes]
rs1115660	0.87[AFR][1000 genomes]
rs12459176	0.89[AFR][1000 genomes]
rs12460429	0.89[AFR][1000 genomes]
rs1428177	0.88[AFR][1000 genomes]
rs1457854	0.89[AFR][1000 genomes]
rs1457855	0.89[AFR][1000 genomes]
rs1457856	0.89[AFR][1000 genomes]
rs1457857	0.85[AFR][1000 genomes]
rs1599602	1.00[EUR][1000 genomes]
rs1817266	0.86[AFR][1000 genomes]
rs1840997	0.88[AFR][1000 genomes]
rs1840998	0.88[AFR][1000 genomes]
rs1864019	0.88[AFR][1000 genomes]
rs2115101	0.89[AFR][1000 genomes]
rs2168792	0.89[AFR][1000 genomes]
rs2903895	0.86[AFR][1000 genomes]
rs324093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324102	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324105	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs326450	1.00[EUR][1000 genomes]
rs35170850	0.88[AFR][1000 genomes]
rs4802949	0.88[AFR][1000 genomes]
rs4802950	0.84[AFR][1000 genomes]
rs59465772	1.00[EUR][1000 genomes]
rs60186879	1.00[EUR][1000 genomes]
rs60952057	1.00[EUR][1000 genomes]
rs61039331	1.00[EUR][1000 genomes]
rs6509641	0.86[AFR][1000 genomes]
rs6509643	0.90[AFR][1000 genomes]
rs7252655	0.88[AFR][1000 genomes]
rs8101762	1.00[EUR][1000 genomes]
rs8110920	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3415774	chr19:52938189-52970794	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52954000-52961600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr19:52954400-52961400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:52954400-52962600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:52954600-52956800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:52955600-52957800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
6	chr19:52955800-52957800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
7	chr19:52955800-52958200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
8	chr19:52955800-52961400	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr19:52956000-52957000	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr19:52956000-52957200	Active TSS	Brain Anterior Caudate	brain
11	chr19:52956000-52957600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:52956000-52958000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
13	chr19:52956000-52969600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:52956000-52986200	ZNF genes & repeats	Liver	Liver
15	chr19:52956200-52957000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:52956200-52957000	Active TSS	Brain Angular Gyrus	brain
17	chr19:52956200-52957200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:52956200-52957200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:52956200-52957200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
20	chr19:52956200-52957200	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr19:52956200-52957200	Active TSS	Fetal Heart	heart
22	chr19:52956200-52957200	Active TSS	Right Ventricle	heart
23	chr19:52956200-52957400	Active TSS	Fetal Brain Male	brain
24	chr19:52956200-52957600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:52956200-52957600	Active TSS	Fetal Kidney	kidney
26	chr19:52956200-52957600	ZNF genes & repeats	NHEK	skin
27	chr19:52956200-52957800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:52956200-52958000	Active TSS	NHDF-Ad	bronchial
29	chr19:52956200-52958200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
30	chr19:52956200-52958400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:52956200-52958400	Active TSS	Psoas Muscle	Psoas
32	chr19:52956200-52961400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr19:52956200-52961400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:52956200-52961600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:52956200-52962800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
36	chr19:52956400-52956800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:52956400-52956800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:52956400-52957000	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr19:52956400-52957000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:52956400-52957000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:52956400-52957000	Active TSS	Brain Substantia Nigra	brain
42	chr19:52956400-52957000	Active TSS	Fetal Muscle Trunk	muscle
43	chr19:52956400-52957000	Active TSS	Left Ventricle	heart
44	chr19:52956400-52957000	Active TSS	Pancreas	Pancrea
45	chr19:52956400-52957000	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr19:52956400-52957000	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr19:52956400-52957200	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr19:52956400-52957200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr19:52956400-52957200	Active TSS	Colon Smooth Muscle	Colon
50	chr19:52956400-52957200	Active TSS	Duodenum Smooth Muscle	Duodenum

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