Variant report

Variant	rs234321
Chromosome Location	chr19:40502611-40502612
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	RUNX3	chr19:40502102-40504096	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:40502306-40503299	HUVEC	blood vessel:	n/a	n/a
3	BACH1	chr19:40502370-40502946	K562	blood:	n/a	n/a
4	POLR2A	chr19:40502498-40503266	A549	lung:	n/a	n/a
5	MAX	chr19:40502257-40503496	GM12878	blood:	n/a	n/a
6	YY1	chr19:40502525-40503304	GM12891	blood:	n/a	chr19:40502905-40502914
7	POLR2A	chr19:40502238-40503667	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:40502214-40503401	HUVEC	blood vessel:	n/a	n/a
9	MYC	chr19:40502250-40503458	K562	blood:	n/a	n/a
10	MYC	chr19:40502559-40503203	HUVEC	blood vessel:	n/a	n/a
11	ZC3H11A	chr19:40502198-40503306	K562	blood:	n/a	n/a
12	MAX	chr19:40502342-40503466	ECC-1	luminal epithelium:	n/a	n/a
13	ELF1	chr19:40502495-40503313	MCF-7	breast:	n/a	chr19:40502905-40502914
14	YY1	chr19:40502337-40503379	GM12878	blood:	n/a	chr19:40502905-40502914
15	CEBPB	chr19:40502224-40503241	Hela-S3	cervix:	n/a	n/a
16	MYBL2	chr19:40502521-40503154	HepG2	liver:	n/a	chr19:40503006-40503016 chr19:40503023-40503033
17	TEAD4	chr19:40502141-40503569	K562	blood:	n/a	n/a
18	FOXA2	chr19:40502306-40503585	A549	lung:	n/a	n/a
19	MTA3	chr19:40502157-40503887	GM12878	blood:	n/a	n/a
20	TCF12	chr19:40502056-40503471	A549	lung:	n/a	chr19:40503367-40503376
21	HDAC2	chr19:40502531-40503105	HepG2	liver:	n/a	chr19:40502891-40502900
22	HEY1	chr19:40502485-40503374	K562	blood:	n/a	n/a
23	POLR2A	chr19:40502268-40503435	GM12878	blood:	n/a	n/a
24	MAX	chr19:40502367-40503387	K562	blood:	n/a	n/a
25	NRF1	chr19:40501772-40503798	SK-N-SH	brain:	n/a	chr19:40502894-40502908 chr19:40502897-40502908 chr19:40502897-40502908
26	JUND	chr19:40502205-40503249	A549	lung:	n/a	chr19:40502524-40502532 chr19:40502522-40502534 chr19:40502525-40502536
27	CREB1	chr19:40502210-40503595	HepG2	liver:	n/a	n/a
28	HCFC1	chr19:40502349-40503596	K562	blood:	n/a	n/a
29	POLR2A	chr19:40502506-40503378	A549	lung:	n/a	n/a
30	GABPA	chr19:40502148-40503568	A549	lung:	n/a	chr19:40502894-40502908 chr19:40502897-40502908
31	TCF7L2	chr19:40502278-40503245	HCT-116	colon:	n/a	n/a
32	POU2F2	chr19:40502218-40503529	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:40502345-40503454	GM19193	blood:	n/a	n/a
34	MAX	chr19:40501659-40503808	A549	lung:	n/a	chr19:40502187-40502196
35	GABPA	chr19:40502194-40503646	A549	lung:	n/a	chr19:40502894-40502908 chr19:40502897-40502908
36	GABPA	chr19:40502466-40503636	HL-60	blood:	n/a	chr19:40502894-40502908 chr19:40502897-40502908
37	E2F6	chr19:40502158-40503659	A549	lung:	n/a	chr19:40502898-40502907
38	ELF1	chr19:40502332-40503528	GM12878	blood:	n/a	chr19:40502905-40502914
39	STAT5A	chr19:40502092-40503769	GM12878	blood:	n/a	chr19:40502941-40502961 chr19:40502947-40502955 chr19:40502944-40502958
40	PML	chr19:40502344-40503053	GM12878	blood:	n/a	n/a
41	MAX	chr19:40501779-40503635	A549	lung:	n/a	chr19:40502187-40502196
42	RCOR1	chr19:40502259-40503550	GM12878	blood:	n/a	n/a
43	STAT3	chr19:40502259-40503065	MCF10A-Er-Src	breast:	n/a	chr19:40502941-40502961 chr19:40502947-40502955 chr19:40502944-40502958
44	POLR2A	chr19:40502164-40503848	GM12878	blood:	n/a	n/a
45	ETS1	chr19:40502148-40503616	A549	lung:	n/a	chr19:40502938-40502951 chr19:40502927-40502936 chr19:40502549-40502566
46	FOSL2	chr19:40502141-40503168	A549	lung:	n/a	chr19:40502524-40502532 chr19:40502522-40502534 chr19:40502525-40502536
47	POLR2A	chr19:40502607-40503060	H1-hESC	embryonic stem cell:	n/a	n/a
48	MAZ	chr19:40502402-40503510	K562	blood:	n/a	n/a
49	YY1	chr19:40502302-40503176	GM12892	blood:	n/a	chr19:40502905-40502914
50	ATF3	chr19:40502340-40503729	A549	lung:	n/a	chr19:40502880-40502888

No.	Distal block	Cell Line	Cell type
1	chr19:40497251..40499736-chr19:40500341..40503901,5	K562	blood:
2	chr19:40502294..40503047-chr6:74230491..74231096,2	Hela-S3	cervix:
3	chr19:40502177..40502746-chr5:6378448..6379167,2	Hela-S3	cervix:
4	chr15:50716516..50717182-chr19:40501949..40502848,2	Hela-S3	cervix:
5	chr1:202075247..202076160-chr19:40502360..40502872,2	Hela-S3	cervix:
6	chr19:40475224..40479165-chr19:40500138..40503908,5	MCF-7	breast:
7	chr18:47900863..47901725-chr19:40502401..40503201,2	HCT-116	colon:
8	chr19:40502301..40502820-chr9:135544860..135545626,2	Hela-S3	cervix:
9	chr19:40475223..40478471-chr19:40501440..40504433,4	MCF-7	breast:
10	chr19:40474074..40479560-chr19:40500872..40505885,15	K562	blood:
11	chr19:40471803..40479510-chr19:40500414..40506141,13	K562	blood:
12	chr14:91976300..91976912-chr19:40501886..40502806,2	Hela-S3	cervix:
13	chr19:40501923..40502863-chr8:42195746..42196717,2	Hela-S3	cervix:
14	chr19:40501950..40503610-chr19:40595158..40598072,2	K562	blood:
15	chr19:40497431..40499811-chr19:40501721..40503252,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF780B-2	chr19:40497983-40502942	NONHSAT066331

Variant related genes	Relation type
ENSG00000221233	TF binding region
ZNF546	TF binding region
ENSG00000070501	Chromatin interaction
ENSG00000269296	Chromatin interaction
ENSG00000125484	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000269749	Chromatin interaction
ENSG00000125485	Chromatin interaction
ENSG00000133398	Chromatin interaction
ENSG00000197782	Chromatin interaction
ENSG00000100796	Chromatin interaction
ENSG00000154839	Chromatin interaction
ENSG00000221233	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10410695	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418448	1.00[EUR][1000 genomes]
rs10419218	1.00[EUR][1000 genomes]
rs10420514	1.00[EUR][1000 genomes]
rs10420687	1.00[EUR][1000 genomes]
rs10421243	1.00[EUR][1000 genomes]
rs10423298	1.00[EUR][1000 genomes]
rs10423800	1.00[EUR][1000 genomes]
rs10427117	1.00[EUR][1000 genomes]
rs11883159	1.00[EUR][1000 genomes]
rs13382054	1.00[EUR][1000 genomes]
rs170898	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234297	1.00[EUR][1000 genomes]
rs234307	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs234312	1.00[EUR][1000 genomes]
rs234316	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234319	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234322	0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234327	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234338	0.84[ASW][hapmap]
rs234339	0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234342	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234359	0.84[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs2531363	0.81[YRI][hapmap]
rs2542302	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs2542311	0.92[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs28589691	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28661993	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28776318	1.00[EUR][1000 genomes]
rs28832070	1.00[EUR][1000 genomes]
rs337795	1.00[EUR][1000 genomes]
rs57342065	1.00[EUR][1000 genomes]
rs58348431	1.00[EUR][1000 genomes]
rs59707868	1.00[EUR][1000 genomes]
rs60631264	1.00[EUR][1000 genomes]
rs61424085	1.00[EUR][1000 genomes]
rs7245930	1.00[EUR][1000 genomes]
rs7250945	1.00[EUR][1000 genomes]
rs7257627	1.00[EUR][1000 genomes]
rs7258111	1.00[EUR][1000 genomes]
rs73930675	1.00[EUR][1000 genomes]
rs73930678	1.00[EUR][1000 genomes]
rs73930679	1.00[EUR][1000 genomes]
rs8111518	1.00[EUR][1000 genomes]
rs8111741	1.00[EUR][1000 genomes]
rs9630860	1.00[EUR][1000 genomes]
rs9630868	1.00[EUR][1000 genomes]
rs9783944	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 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	chr19:40501600-40503000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:40501600-40503200	Active TSS	Fetal Brain Female	brain
3	chr19:40501600-40503200	Active TSS	NHEK	skin
4	chr19:40501600-40503200	Active TSS	NHLF	lung
5	chr19:40501600-40503400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:40501600-40503400	Active TSS	A549	lung
7	chr19:40501600-40503600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:40501800-40503000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:40501800-40503200	Active TSS	Fetal Brain Male	brain
10	chr19:40501800-40503400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr19:40501800-40503400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:40501800-40503400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:40501800-40503400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr19:40501800-40503400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:40501800-40503400	Active TSS	Brain Hippocampus Middle	brain
16	chr19:40501800-40503400	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr19:40501800-40503400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:40501800-40503400	Active TSS	K562	blood
19	chr19:40501800-40503600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr19:40501800-40503600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:40501800-40503600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr19:40501800-40503600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr19:40501800-40503600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:40501800-40503600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:40501800-40503600	Active TSS	NHDF-Ad	bronchial
26	chr19:40501800-40503800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr19:40501800-40503800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr19:40501800-40504000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:40502000-40503000	Active TSS	Muscle Satellite Cultured Cells	--
30	chr19:40502000-40503000	Active TSS	HSMM	muscle
31	chr19:40502000-40503200	Active TSS	Duodenum Mucosa	Duodenum
32	chr19:40502000-40503200	Active TSS	Hela-S3	cervix
33	chr19:40502000-40503400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:40502000-40503400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:40502000-40503400	Active TSS	Liver	Liver
36	chr19:40502000-40503400	Active TSS	Colon Smooth Muscle	Colon
37	chr19:40502000-40503400	Active TSS	Right Ventricle	heart
38	chr19:40502000-40503600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr19:40502000-40503600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:40502000-40503600	Active TSS	Fetal Intestine Large	intestine
41	chr19:40502000-40503600	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr19:40502000-40503800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:40502000-40503800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr19:40502000-40503800	Active TSS	Fetal Intestine Small	intestine
45	chr19:40502000-40503800	Active TSS	Fetal Kidney	kidney
46	chr19:40502000-40503800	Active TSS	Psoas Muscle	Psoas
47	chr19:40502200-40502800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr19:40502200-40502800	Active TSS	Right Atrium	heart
49	chr19:40502200-40503000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:40502200-40503000	Active TSS	Colonic Mucosa	Colon

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