Variant report

Variant	rs379722
Chromosome Location	chr19:44439422-44439423
allele	A/C
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	POLR2A	chr19:44439114-44439812	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr19:44439184-44439497	H1-hESC	embryonic stem cell:	n/a	n/a
3	POU2F2	chr19:44439390-44439641	GM12878	blood:	n/a	n/a
4	WRNIP1	chr19:44439215-44439765	GM12878	blood:	n/a	n/a
5	ETS1	chr19:44439012-44439926	A549	lung:	n/a	chr19:44439422-44439431 chr19:44439510-44439520 chr19:44439707-44439720 chr19:44439497-44439508 chr19:44439509-44439518 chr19:44439415-44439431 chr19:44439455-44439468 chr19:44439422-44439433 chr19:44439509-44439520 chr19:44439520-44439533 chr19:44439423-44439433 chr19:44439454-44439467 chr19:44439483-44439490
6	POLR2A	chr19:44439033-44440063	HepG2	liver:	n/a	n/a
7	MAZ	chr19:44438950-44439853	K562	blood:	n/a	n/a
8	YY1	chr19:44439138-44439649	GM12892	blood:	n/a	chr19:44439497-44439506
9	SPI1	chr19:44439181-44439716	HL-60	blood:	n/a	n/a
10	SPI1	chr19:44439007-44439854	HL-60	blood:	n/a	n/a
11	SIX5	chr19:44439289-44439899	H1-hESC	embryonic stem cell:	n/a	chr19:44439458-44439467 chr19:44439456-44439465 chr19:44439454-44439468
12	POLR2A	chr19:44438871-44439765	MCF10A-Er-Src	breast:	n/a	n/a
13	TAF1	chr19:44439022-44439963	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr19:44439346-44439651	H1-hESC	embryonic stem cell:	n/a	chr19:44439497-44439506
15	GABPA	chr19:44438817-44440161	A549	lung:	n/a	chr19:44439497-44439506
16	MAX	chr19:44439217-44439941	GM12878	blood:	n/a	n/a
17	IRF1	chr19:44439255-44439719	K562	blood:	n/a	chr19:44439493-44439507
18	ARID3A	chr19:44439324-44439570	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:44439047-44439765	ECC-1	luminal epithelium:	n/a	n/a
20	ETS1	chr19:44439299-44439593	K562	blood:	n/a	chr19:44439422-44439431 chr19:44439510-44439520 chr19:44439497-44439508 chr19:44439509-44439518 chr19:44439415-44439431 chr19:44439455-44439468 chr19:44439422-44439433 chr19:44439509-44439520 chr19:44439520-44439533 chr19:44439423-44439433 chr19:44439454-44439467 chr19:44439483-44439490
21	MAX	chr19:44439000-44439887	K562	blood:	n/a	n/a
22	POLR2A	chr19:44439083-44439844	PANC-1	pancreas:	n/a	n/a
23	ELF1	chr19:44438975-44439872	MCF-7	breast:	n/a	chr19:44439418-44439431 chr19:44439263-44439275
24	POLR2A	chr19:44438976-44439945	SK-N-SH	brain:	n/a	n/a
25	STAT3	chr19:44439392-44439637	MCF10A-Er-Src	breast:	n/a	chr19:44439546-44439560
26	SIN3AK20	chr19:44439068-44439722	A549	lung:	n/a	n/a
27	CHD2	chr19:44439075-44439850	K562	blood:	n/a	n/a
28	ELF1	chr19:44439129-44439787	A549	lung:	n/a	chr19:44439418-44439431 chr19:44439263-44439275
29	POLR2A	chr19:44438968-44439972	SK-N-MC	brain:	n/a	n/a
30	E2F4	chr19:44439355-44439907	GM12878	blood:	n/a	chr19:44439741-44439753 chr19:44439497-44439506
31	ZNF143	chr19:44439106-44439926	GM12878	blood:	n/a	chr19:44439458-44439467 chr19:44439709-44439727 chr19:44439456-44439474 chr19:44439456-44439465
32	POLR2A	chr19:44439121-44439646	HepG2	liver:	n/a	n/a
33	CTCF	chr19:44439180-44439470	GM12872	blood:	n/a	chr19:44439265-44439278
34	BCLAF1	chr19:44439099-44439875	GM12878	blood:	n/a	chr19:44439269-44439278 chr19:44439509-44439518 chr19:44439485-44439498
35	POLR2A	chr19:44438957-44439988	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:44439060-44439784	HepG2	liver:	n/a	n/a
37	YY1	chr19:44439054-44439648	HepG2	liver:	n/a	chr19:44439497-44439506
38	JUND	chr19:44439021-44439808	K562	blood:	n/a	chr19:44439761-44439773 chr19:44439368-44439379 chr19:44439565-44439574
39	POLR2A	chr19:44439077-44439681	K562	blood:	n/a	n/a
40	POLR2A	chr19:44439145-44439741	HCT-116	colon:	n/a	n/a
41	GATA3	chr19:44438899-44440131	A549	lung:	n/a	chr19:44439290-44439300
42	RCOR1	chr19:44439186-44439847	GM12878	blood:	n/a	n/a
43	ELF1	chr19:44439017-44439765	K562	blood:	n/a	chr19:44439418-44439431 chr19:44439263-44439275
44	POLR2A	chr19:44439093-44439646	A549	lung:	n/a	n/a
45	CEBPB	chr19:44439252-44439441	H1-hESC	embryonic stem cell:	n/a	n/a
46	ETS1	chr19:44439189-44439795	GM12878	blood:	n/a	chr19:44439422-44439431 chr19:44439510-44439520 chr19:44439707-44439720 chr19:44439497-44439508 chr19:44439509-44439518 chr19:44439415-44439431 chr19:44439455-44439468 chr19:44439422-44439433 chr19:44439509-44439520 chr19:44439520-44439533 chr19:44439423-44439433 chr19:44439454-44439467 chr19:44439483-44439490
47	GABPA	chr19:44439038-44439821	HepG2	liver:	n/a	chr19:44439497-44439506
48	POLR2A	chr19:44439024-44439787	ECC-1	luminal epithelium:	n/a	n/a
49	GABPA	chr19:44439221-44439714	H1-hESC	embryonic stem cell:	n/a	chr19:44439497-44439506
50	POLR2A	chr19:44439065-44439777	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44439254..44441098-chr19:44452141..44456291,4	K562	blood:
2	chr19:44405165..44406844-chr19:44438913..44440753,2	K562	blood:
3	chr19:44330249..44332710-chr19:44437495..44440338,2	MCF-7	breast:
4	chr19:44438985..44440520-chr19:44510451..44513064,2	MCF-7	breast:
5	chr19:44330466..44332260-chr19:44438054..44440025,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF45-1	chr19:44439382-44439430	NONHSAT066644

Variant related genes	Relation type
ZNF45	TF binding region
ENSG00000167637	Chromatin interaction
ENSG00000267058	Chromatin interaction
ENSG00000159905	Chromatin interaction
ENSG00000267191	Chromatin interaction
ENSG00000159871	Chromatin interaction
ENSG00000176222	Chromatin interaction
ENSG00000159882	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs364378	0.87[AMR][1000 genomes]
rs364693	0.87[AMR][1000 genomes]
rs365769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs367056	0.89[AMR][1000 genomes]
rs367241	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs373043	0.89[AMR][1000 genomes]
rs376769	0.87[AMR][1000 genomes]
rs382715	0.87[AMR][1000 genomes]
rs384432	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs393403	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs393473	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs395143	0.87[AMR][1000 genomes]
rs424364	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs441225	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs442934	0.89[AMR][1000 genomes]
rs446072	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs452143	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs453611	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs461374	0.87[AMR][1000 genomes]
rs465860	0.87[AMR][1000 genomes]
rs8101844	0.87[AMR][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	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
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 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	chr19:44438000-44439800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:44438000-44440000	Active TSS	GM12878-XiMat	blood
3	chr19:44438000-44440000	Active TSS	NHLF	lung
4	chr19:44438200-44439800	Active TSS	Hela-S3	cervix
5	chr19:44438200-44440000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:44438200-44440200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr19:44438200-44440200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:44438200-44440200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:44438200-44440200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr19:44438200-44440200	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr19:44438200-44440200	Active TSS	Psoas Muscle	Psoas
12	chr19:44438200-44440600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:44438400-44439800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:44438400-44439800	Active TSS	Fetal Kidney	kidney
15	chr19:44438400-44439800	Active TSS	Lung	lung
16	chr19:44438400-44440000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:44438400-44440000	Active TSS	Right Atrium	heart
18	chr19:44438400-44440000	Active TSS	Right Ventricle	heart
19	chr19:44438400-44440200	Active TSS	Fetal Intestine Small	intestine
20	chr19:44438600-44439600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:44438600-44439800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:44438600-44439800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:44438600-44439800	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr19:44438600-44440000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr19:44438600-44440000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr19:44438600-44440000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:44438600-44440000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:44438600-44440000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:44438600-44440000	Active TSS	Aorta	Aorta
30	chr19:44438600-44440000	Active TSS	Fetal Brain Female	brain
31	chr19:44438600-44440000	Active TSS	NHDF-Ad	bronchial
32	chr19:44438600-44440200	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:44438600-44440600	Active TSS	Thymus	Thymus
34	chr19:44438800-44439600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:44438800-44439600	Active TSS	Primary monocytes fromperipheralblood	blood
36	chr19:44438800-44439600	Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr19:44438800-44439600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr19:44438800-44439600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:44438800-44439600	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:44438800-44439600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:44438800-44439600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr19:44438800-44439600	Active TSS	Dnd41	blood
43	chr19:44438800-44439800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr19:44438800-44439800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:44438800-44439800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:44438800-44439800	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr19:44438800-44439800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:44438800-44439800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:44438800-44439800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr19:44438800-44439800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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