Variant report

Variant	rs3826705
Chromosome Location	chr19:42637232-42637233
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	MAZ	chr19:42635501-42637934	IMR90	lung:	n/a	chr19:42637456-42637466 chr19:42637679-42637688 chr19:42637428-42637438
2	SP1	chr19:42637134-42637649	GM12878	blood:	n/a	chr19:42637456-42637470 chr19:42637463-42637477 chr19:42637428-42637438 chr19:42637424-42637438 chr19:42637455-42637467 chr19:42637429-42637438 chr19:42637427-42637438 chr19:42637455-42637466 chr19:42637455-42637467 chr19:42637427-42637439 chr19:42637428-42637437 chr19:42637427-42637439
3	MXI1	chr19:42637091-42637840	H1-hESC	embryonic stem cell:	n/a	n/a
4	SMC3	chr19:42636748-42638211	SK-N-SH	brain:	n/a	chr19:42637392-42637406
5	ELK1	chr19:42637197-42637549	GM12878	blood:	n/a	n/a
6	RAD21	chr19:42636871-42637829	A549	lung:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637578-42637590 chr19:42637391-42637410 chr19:42637396-42637406
7	CTCF	chr19:42637183-42637568	GM19238	blood:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
8	YY1	chr19:42637081-42637651	GM12892	blood:	n/a	chr19:42637431-42637445 chr19:42637425-42637439
9	RUNX3	chr19:42636317-42637898	GM12878	blood:	n/a	n/a
10	CTCF	chr19:42637006-42637641	A549	lung:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
11	CTCF	chr19:42637168-42637556	ECC-1	luminal epithelium:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
12	RAD21	chr19:42637177-42637599	GM12878	blood:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637578-42637590 chr19:42637391-42637410 chr19:42637396-42637406
13	SMC3	chr19:42637189-42637643	K562	blood:	n/a	chr19:42637392-42637406
14	EP300	chr19:42636911-42637485	GM12878	blood:	n/a	n/a
15	RAD21	chr19:42637041-42637801	H1-hESC	embryonic stem cell:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637578-42637590 chr19:42637391-42637410 chr19:42637396-42637406
16	ZNF263	chr19:42636949-42637578	HEK293-T-REx	kidney:	n/a	n/a
17	EBF1	chr19:42637014-42637316	GM12878	blood:	n/a	n/a
18	EBF1	chr19:42636912-42637409	GM12878	blood:	n/a	n/a
19	JUND	chr19:42637134-42637632	A549	lung:	n/a	n/a
20	CTCF	chr19:42637100-42637250	AoAF	blood vessel:	n/a	n/a
21	CTBP2	chr19:42637063-42637714	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr19:42637069-42637800	MCF-7	breast:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637578-42637590 chr19:42637391-42637410 chr19:42637396-42637406
23	RAD21	chr19:42637078-42637756	ECC-1	luminal epithelium:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637578-42637590 chr19:42637391-42637410 chr19:42637396-42637406
24	YY1	chr19:42637126-42637580	GM12878	blood:	n/a	chr19:42637431-42637445 chr19:42637425-42637439
25	RCOR1	chr19:42636771-42637574	GM12878	blood:	n/a	n/a
26	BACH1	chr19:42636880-42637644	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAZ	chr19:42635991-42637781	GM12878	blood:	n/a	chr19:42637456-42637466 chr19:42637679-42637688 chr19:42637428-42637438
28	SP1	chr19:42637186-42637653	H1-hESC	embryonic stem cell:	n/a	chr19:42637456-42637470 chr19:42637463-42637477 chr19:42637428-42637438 chr19:42637424-42637438 chr19:42637455-42637467 chr19:42637429-42637438 chr19:42637427-42637438 chr19:42637455-42637466 chr19:42637455-42637467 chr19:42637427-42637439 chr19:42637428-42637437 chr19:42637427-42637439
29	CHD1	chr19:42637189-42637495	GM12878	blood:	n/a	n/a
30	RAD21	chr19:42637122-42637625	HepG2	liver:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637578-42637590 chr19:42637391-42637410 chr19:42637396-42637406
31	ETS1	chr19:42637199-42637590	A549	lung:	n/a	chr19:42637205-42637219 chr19:42637206-42637213 chr19:42637206-42637217
32	CEBPB	chr19:42636910-42637508	H1-hESC	embryonic stem cell:	n/a	n/a
33	RELA	chr19:42636415-42637602	GM19099	blood:	n/a	n/a
34	CTCF	chr19:42637217-42637598	HepG2	liver:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
35	JUN	chr19:42637156-42637475	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr19:42637095-42637641	H1-hESC	embryonic stem cell:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637578-42637590 chr19:42637391-42637410 chr19:42637396-42637406
37	TCF12	chr19:42637168-42637649	GM12878	blood:	n/a	n/a
38	RAD21	chr19:42637210-42637577	K562	blood:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637391-42637410 chr19:42637396-42637406
39	STAT5A	chr19:42635175-42638001	GM12878	blood:	n/a	chr19:42637467-42637479 chr19:42636457-42636469 chr19:42636651-42636659
40	RAD21	chr19:42637217-42637577	Hela-S3	cervix:	n/a	chr19:42637396-42637408 chr19:42637394-42637407 chr19:42637391-42637410 chr19:42637396-42637406
41	TBP	chr19:42637054-42637723	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr19:42637108-42637581	GM12892	blood:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
43	CTCF	chr19:42637131-42637739	K562	blood:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
44	CTCF	chr19:42637132-42637556	K562	blood:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
45	POLR2A	chr19:42637192-42637362	GM12878	blood:	n/a	n/a
46	CTCF	chr19:42637113-42637628	H1-hESC	embryonic stem cell:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
47	CTCF	chr19:42637231-42637233	Pancreas_OC	pancreas:	n/a	n/a
48	CTCF	chr19:42636957-42638253	SK-N-SH	brain:	n/a	chr19:42637390-42637408 chr19:42637393-42637406 chr19:42637393-42637406
49	PAX5	chr19:42637137-42637634	GM12892	blood:	n/a	chr19:42637205-42637214 chr19:42637585-42637594
50	TCF7L2	chr19:42636918-42637522	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42633522..42638694-chr19:42746138..42750554,7	MCF-7	breast:
2	chr19:42636828..42637661-chr19:42794793..42795501,2	MCF-7	breast:
3	chr19:42636942..42637484-chr19:42748872..42749487,2	MCF-7	breast:
4	chr19:42636373..42638915-chr19:42720548..42722250,2	K562	blood:
5	chr19:42635908..42637721-chr19:42758077..42760755,2	K562	blood:
6	chr19:42634611..42641780-chr19:42741001..42747645,8	MCF-7	breast:
7	chr19:42634645..42637332-chr19:42721658..42723900,2	K562	blood:
8	chr19:42636888..42637505-chr19:42828599..42829878,4	K562	blood:

Variant related genes	Relation type
ENSG00000254887	TF binding region
POU2F2	TF binding region
ENSG00000105723	Chromatin interaction
ENSG00000204957	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000268643	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000105429	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10407506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10500285	0.81[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11878620	0.86[GIH][hapmap]
rs11878917	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11880124	0.85[CHD][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs11883412	0.85[CHD][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs12232804	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16975663	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs16975684	0.89[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs17270057	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17270169	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17342067	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17342179	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17342284	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2217342	0.80[TSI][hapmap]
rs2302485	0.86[GIH][hapmap]
rs2303652	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs3736109	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs3745231	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs3745233	0.93[GIH][hapmap]
rs3810151	0.89[CEU][hapmap]
rs4141062	0.86[GIH][hapmap]
rs443239	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs454150	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs4803520	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7248379	0.89[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs7251466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes]
rs7253767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106871	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182491	0.89[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs899661	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3826705	ZNF219	trans	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42633400-42638000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:42634000-42637400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:42634000-42637800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
4	chr19:42634200-42638000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr19:42635400-42637600	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr19:42635400-42637800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr19:42635400-42637800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:42635400-42637800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:42635400-42638000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr19:42635400-42638000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr19:42635400-42638000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:42635400-42638200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr19:42635400-42638200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:42635600-42637400	Flanking Active TSS	NHEK	skin
15	chr19:42635600-42637600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
16	chr19:42635600-42637600	Active TSS	Right Atrium	heart
17	chr19:42636000-42637600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:42636000-42637800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:42636000-42637800	Flanking Active TSS	Fetal Thymus	thymus
20	chr19:42636000-42638000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:42636200-42637400	Flanking Active TSS	NH-A	brain
22	chr19:42636200-42637600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:42636200-42637600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr19:42636200-42637600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:42636200-42637800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr19:42636200-42637800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr19:42636200-42637800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:42636400-42637600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
29	chr19:42636400-42637600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
30	chr19:42636400-42637800	Active TSS	Brain Anterior Caudate	brain
31	chr19:42636600-42637400	Weak transcription	Lung	lung
32	chr19:42636600-42637600	Active TSS	Brain Angular Gyrus	brain
33	chr19:42636600-42637600	Active TSS	Thymus	Thymus
34	chr19:42636600-42637800	Bivalent Enhancer	Fetal Intestine Small	intestine
35	chr19:42636600-42637800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr19:42636600-42638000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr19:42636600-42638200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:42636600-42638800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:42636800-42637400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:42636800-42637400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:42636800-42637400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:42636800-42637400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
43	chr19:42636800-42637400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
44	chr19:42636800-42637400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
45	chr19:42636800-42637400	Flanking Active TSS	NHDF-Ad	bronchial
46	chr19:42636800-42637400	Flanking Active TSS	NHLF	lung
47	chr19:42636800-42637400	Flanking Active TSS	Osteobl	bone
48	chr19:42636800-42637600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
49	chr19:42636800-42637600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr19:42636800-42637600	Flanking Active TSS	HUVEC	blood vessel

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