Variant report

Variant	rs2599459
Chromosome Location	chr19:44037370-44037371
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:368)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:368 , 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	MYC	chr19:44037121-44037782	K562	blood:	n/a	n/a
2	POLR2A	chr19:44036634-44038136	A549	lung:	n/a	n/a
3	MAFK	chr19:44037206-44037534	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:44037038-44038436	HL-60	blood:	n/a	n/a
5	ATF3	chr19:44036698-44037626	A549	lung:	n/a	n/a
6	MYC	chr19:44036850-44037476	MCF10A-Er-Src	breast:	n/a	chr19:44037089-44037099
7	POLR2A	chr19:44037116-44038542	GM12878	blood:	n/a	n/a
8	PML	chr19:44037241-44038337	MCF-7	breast:	n/a	n/a
9	POLR2A	chr19:44036778-44038675	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr19:44037126-44037485	H1-hESC	embryonic stem cell:	n/a	n/a
11	CUX1	chr19:44037280-44037667	GM12878	blood:	n/a	n/a
12	HMGN3	chr19:44037263-44038398	K562	blood:	n/a	n/a
13	STAT1	chr19:44037129-44037675	GM12878	blood:	n/a	n/a
14	MXI1	chr19:44036998-44038007	GM12878	blood:	n/a	n/a
15	TEAD4	chr19:44036618-44037940	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr19:44036630-44038157	GM12878	blood:	n/a	n/a
17	TAF1	chr19:44036707-44037673	A549	lung:	n/a	n/a
18	MAX	chr19:44036703-44037776	SK-N-SH	brain:	n/a	chr19:44037089-44037099
19	ZKSCAN1	chr19:44037192-44037618	Hela-S3	cervix:	n/a	n/a
20	TCF12	chr19:44036427-44037712	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr19:44036742-44038486	GM15510	blood:	n/a	n/a
22	MAX	chr19:44036775-44037673	MCF-7	breast:	n/a	chr19:44037089-44037099
23	PML	chr19:44036741-44038435	GM12878	blood:	n/a	n/a
24	PBX3	chr19:44036843-44037678	A549	lung:	n/a	n/a
25	EBF1	chr19:44036715-44037690	GM12878	blood:	n/a	chr19:44037649-44037658 chr19:44037649-44037658
26	CHD2	chr19:44037331-44037545	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:44037070-44038196	U87	brain:	n/a	n/a
28	ELK1	chr19:44036707-44037773	Hela-S3	cervix:	n/a	n/a
29	ELF1	chr19:44037221-44037831	K562	blood:	n/a	chr19:44037303-44037315 chr19:44037635-44037644
30	NFYB	chr19:44036817-44037705	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:44037040-44038201	GM12892	blood:	n/a	n/a
32	RCOR1	chr19:44037066-44038017	K562	blood:	n/a	n/a
33	USF2	chr19:44037135-44037672	H1-hESC	embryonic stem cell:	n/a	chr19:44037302-44037318
34	NFATC1	chr19:44036779-44038360	GM12878	blood:	n/a	n/a
35	MAZ	chr19:44037341-44037836	HepG2	liver:	n/a	n/a
36	CTCF	chr19:44037287-44037563	GM19239	blood:	n/a	n/a
37	FOXA2	chr19:44036677-44037726	A549	lung:	n/a	n/a
38	ZBTB7A	chr19:44037227-44037776	K562	blood:	n/a	n/a
39	EBF1	chr19:44036832-44038227	GM12878	blood:	n/a	chr19:44037649-44037658 chr19:44037649-44037658 chr19:44038106-44038115 chr19:44038105-44038115
40	MTA3	chr19:44037041-44038072	GM12878	blood:	n/a	n/a
41	CTCF	chr19:44037240-44037390	A549	lung:	n/a	n/a
42	POLR2A	chr19:44036481-44038538	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr19:44037340-44037490	BE2_C	brain:	n/a	n/a
44	CTCF	chr19:44037341-44037700	Spleen_OC	spleen:	n/a	chr19:44037667-44037675
45	MYC	chr19:44037234-44037729	H1-hESC	embryonic stem cell:	n/a	n/a
46	GTF2F1	chr19:44037299-44037761	H1-hESC	embryonic stem cell:	n/a	n/a
47	EGR1	chr19:44037210-44037715	ECC-1	luminal epithelium:	n/a	chr19:44037303-44037313 chr19:44037643-44037653 chr19:44037470-44037480 chr19:44037469-44037483
48	CHD2	chr19:44036919-44038321	Hela-S3	cervix:	n/a	n/a
49	PBX3	chr19:44036821-44037849	A549	lung:	n/a	n/a
50	ZMIZ1	chr19:44037190-44038078	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:44037336-44037386	GM12891	blood:	n/a
2	chr19:44037336-44037386	SK-N-SH_RA	brain:	n/a
3	chr19:44037336-44037386	H1-hESC	embryonic stem cell:	embryo
4	chr19:44037336-44037386	K562	blood:	n/a
5	chr19:44037336-44037386	AG09319	gingival:	n/a
6	chr19:44037336-44037386	PrEC	prostate:	n/a
7	chr19:44037336-44037386	PANC-1	pancreas:	n/a
8	chr19:44037336-44037386	HMEC	breast:	n/a
9	chr19:44037336-44037386	AG04450	lung:	fetal
10	chr19:44037336-44037386	ECC-1	luminal epithelium:	n/a
11	chr19:44037336-44037386	HCF	heart:	n/a
12	chr19:44037336-44037386	BJ	skin:	n/a
13	chr19:44037336-44037386	Hela-S3	cervix:	n/a
14	chr19:44037336-44037386	SKMC	muscle:	n/a
15	chr19:44037336-44037386	HRPEpiC	eye:	n/a
16	chr19:44037336-44037386	HL-60	blood:	n/a
17	chr19:44037336-44037386	LNCaP	prostate:	n/a
18	chr19:44037336-44037386	HNPCEpiC	eye:	n/a
19	chr19:44037336-44037386	AoSMC	blood vessel:	n/a
20	chr19:44037336-44037386	Caco-2	colon:	n/a
21	chr19:44037336-44037386	HRCEpiC	kidney:	n/a
22	chr19:44037336-44037386	HepG2	liver:	n/a
23	chr19:44037336-44037386	HEK293	kidney:	embryo
24	chr19:44037336-44037386	HIPEpiC	eye:	n/a
25	chr19:44037336-44037386	A549	lung:	n/a
26	chr19:44037336-44037386	PFSK-1	brain:	n/a
27	chr19:44037336-44037386	MCF-7	breast:	n/a
28	chr19:44037336-44037386	NT2-D1	testis:	n/a
29	chr19:44037336-44037386	U87	brain:	n/a
30	chr19:44037336-44037386	ProgFib	skin:	n/a
31	chr19:44037336-44037386	GM12892	blood:	n/a
32	chr19:44037336-44037386	IMR90	lung:	fetal
33	chr19:44037336-44037386	AG10803	skin:	n/a
34	chr19:44037336-44037386	Hepatocyte	liver:	n/a
35	chr19:44037336-44037386	NB4	blood:	n/a
36	chr19:44037336-44037386	NH-A	brain:	n/a
37	chr19:44037336-44037386	CMK	blood:	n/a
38	chr19:44037336-44037386	HRE	kidney:	n/a
39	chr19:44037336-44037386	GM06990	blood:	n/a
40	chr19:44037336-44037386	SK-N-MC	brain:	n/a
41	chr19:44037336-44037386	MCF10A-Er-Src	breast:	n/a
42	chr19:44037336-44037386	HCPEpiC	choroid plexus:	n/a
43	chr19:44037336-44037386	HCT-116	colon:	n/a
44	chr19:44037336-44037386	GM12878	blood:	n/a
45	chr19:44037336-44037386	T-47D	breast:	n/a
46	chr19:44037336-44037386	RPTEC	kidney:	n/a
47	chr19:44037336-44037386	HPAEpiC	pulmonary alveolar:	n/a
48	chr19:44037336-44037386	HCM	heart:	n/a
49	chr19:44037336-44037386	HAEpiC	amniotic membrane:	n/a
50	chr19:44037336-44037386	AG04449	skin:	fetal

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44036740..44039638-chr19:44122133..44124023,3	MCF-7	breast:
2	chr19:43967717..43971076-chr19:44036987..44039699,3	MCF-7	breast:
3	chr19:44036787..44038928-chr19:44171420..44173895,2	K562	blood:
4	chr19:44036203..44038928-chr19:44171420..44174647,3	K562	blood:
5	chr19:44007568..44009583-chr19:44036201..44039639,3	MCF-7	breast:
6	chr19:44035923..44038107-chr19:44078243..44080720,2	MCF-7	breast:
7	chr19:44036629..44040127-chr19:44122528..44124622,4	K562	blood:
8	chr19:44036185..44038265-chr19:44078295..44081409,3	K562	blood:
9	chr19:44036790..44040633-chr19:44098075..44102401,5	K562	blood:
10	chr19:44036790..44039764-chr19:44099068..44102401,4	K562	blood:
11	chr19:44036736..44038487-chr19:44172015..44174560,2	MCF-7	breast:
12	chr19:44029247..44034379-chr19:44035166..44038879,9	MCF-7	breast:
13	chr19:44036786..44040035-chr19:44171480..44174677,5	MCF-7	breast:
14	chr19:44029421..44031405-chr19:44036593..44038198,2	K562	blood:

No data

Variant related genes	Relation type
ZNF575	TF binding region
ZNF575	CpG island
ENSG00000105755	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000269583	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000011422	Chromatin interaction
ENSG00000124466	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11407	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2021092	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs25484	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2599464	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682552	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2682560	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682587	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2854495	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2854496	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2854498	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2854502	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2854505	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2854510	0.85[EUR][1000 genomes]
rs304729	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs304730	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3213283	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3213285	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3213289	0.85[EUR][1000 genomes]
rs3213332	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3213370	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs939460	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv912107	chr19:44030998-44055726	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2599459	ZNF575	cis	Nerve Tibial	GTEx
rs2599459	ZNF575	cis	Skin Sun Exposed Lower leg	GTEx
rs2599459	ZNF575	cis	Adipose Subcutaneous	GTEx
rs2599459	ZNF575	cis	Artery Tibial	GTEx
rs2599459	ENSG00000176472	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44036200-44038200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr19:44036400-44038000	Flanking Active TSS	Colonic Mucosa	Colon
3	chr19:44036400-44038000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr19:44036400-44038200	Flanking Active TSS	Liver	Liver
5	chr19:44036400-44038400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:44036400-44038400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:44036400-44038600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:44036400-44038600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:44036400-44038800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:44036400-44038800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr19:44036400-44039000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:44036400-44039000	Active TSS	Brain Angular Gyrus	brain
13	chr19:44036600-44037400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr19:44036600-44037400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:44036600-44037400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr19:44036600-44037400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr19:44036600-44037400	Active TSS	Esophagus	oesophagus
18	chr19:44036600-44037400	Flanking Active TSS	Fetal Thymus	thymus
19	chr19:44036600-44037400	Active TSS	Right Ventricle	heart
20	chr19:44036600-44037400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr19:44036600-44037400	Flanking Active TSS	Hela-S3	cervix
22	chr19:44036600-44037600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:44036600-44038000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr19:44036600-44038000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:44036600-44038000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:44036600-44038000	Flanking Active TSS	HUVEC	blood vessel
27	chr19:44036600-44038000	Flanking Active TSS	NHEK	skin
28	chr19:44036600-44038200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr19:44036600-44038200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:44036600-44038400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr19:44036600-44038400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr19:44036600-44038400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr19:44036600-44038400	Active TSS	Brain Anterior Caudate	brain
34	chr19:44036600-44038400	Active TSS	Psoas Muscle	Psoas
35	chr19:44036600-44038600	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr19:44036600-44038600	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr19:44036600-44038600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr19:44036600-44038600	Active TSS	Aorta	Aorta
39	chr19:44036600-44038600	Flanking Active TSS	Placenta	Placenta
40	chr19:44036600-44038600	Active TSS	Right Atrium	heart
41	chr19:44036600-44038800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr19:44036600-44038800	Active TSS	Fetal Kidney	kidney
43	chr19:44036600-44038800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr19:44036600-44038800	Flanking Active TSS	HMEC	breast
45	chr19:44036600-44040200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr19:44036800-44037400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:44036800-44037400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr19:44036800-44037400	Flanking Active TSS	K562	blood
49	chr19:44036800-44038000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:44036800-44038200	Flanking Active TSS	Dnd41	blood

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