Variant report

Variant	rs62126354
Chromosome Location	chr19:55791091-55791092
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	REST	chr19:55791083-55791675	A549	lung:	n/a	chr19:55791448-55791466
2	SP1	chr19:55791062-55791835	K562	blood:	n/a	chr19:55791795-55791804 chr19:55791777-55791791 chr19:55791605-55791617 chr19:55791606-55791620 chr19:55791777-55791787 chr19:55791610-55791622 chr19:55791625-55791637 chr19:55791606-55791615 chr19:55791730-55791739 chr19:55791660-55791672 chr19:55791778-55791787 chr19:55791777-55791786 chr19:55791606-55791616 chr19:55791227-55791237 chr19:55791731-55791740 chr19:55791729-55791741 chr19:55791796-55791805 chr19:55791625-55791637 chr19:55791153-55791160 chr19:55791777-55791786 chr19:55791794-55791806 chr19:55791226-55791238 chr19:55791227-55791237 chr19:55791795-55791805 chr19:55791126-55791140 chr19:55791606-55791616 chr19:55791795-55791805 chr19:55791795-55791804 chr19:55791606-55791615 chr19:55791777-55791787 chr19:55791627-55791636 chr19:55791776-55791788 chr19:55791729-55791741 chr19:55791605-55791617 chr19:55791626-55791640 chr19:55791776-55791788 chr19:55791607-55791616 chr19:55791626-55791635 chr19:55791794-55791806
3	SP1	chr19:55791012-55792074	H1-hESC	embryonic stem cell:	n/a	chr19:55791795-55791804 chr19:55791777-55791791 chr19:55791605-55791617 chr19:55791606-55791620 chr19:55791777-55791787 chr19:55791610-55791622 chr19:55791872-55791882 chr19:55791625-55791637 chr19:55791606-55791615 chr19:55791730-55791739 chr19:55791660-55791672 chr19:55791778-55791787 chr19:55791777-55791786 chr19:55791606-55791616 chr19:55791227-55791237 chr19:55791731-55791740 chr19:55791729-55791741 chr19:55791860-55791867 chr19:55791796-55791805 chr19:55791625-55791637 chr19:55791153-55791160 chr19:55791777-55791786 chr19:55791794-55791806 chr19:55791226-55791238 chr19:55791227-55791237 chr19:55791795-55791805 chr19:55791126-55791140 chr19:55791606-55791616 chr19:55791795-55791805 chr19:55791795-55791804 chr19:55791871-55791883 chr19:55791606-55791615 chr19:55791777-55791787 chr19:55791871-55791883 chr19:55791627-55791636 chr19:55791776-55791788 chr19:55791729-55791741 chr19:55791605-55791617 chr19:55791626-55791640 chr19:55791776-55791788 chr19:55791607-55791616 chr19:55791626-55791635 chr19:55791794-55791806
4	EP300	chr19:55790914-55791740	A549	lung:	n/a	chr19:55791504-55791511 chr19:55791657-55791666
5	POLR2A	chr19:55791068-55791787	U87	brain:	n/a	n/a
6	SP1	chr19:55790980-55792094	A549	lung:	n/a	chr19:55791795-55791804 chr19:55791777-55791791 chr19:55791605-55791617 chr19:55791606-55791620 chr19:55791777-55791787 chr19:55791610-55791622 chr19:55791872-55791882 chr19:55791625-55791637 chr19:55791606-55791615 chr19:55791730-55791739 chr19:55791660-55791672 chr19:55791778-55791787 chr19:55791777-55791786 chr19:55791606-55791616 chr19:55791227-55791237 chr19:55791731-55791740 chr19:55791729-55791741 chr19:55791860-55791867 chr19:55791796-55791805 chr19:55791625-55791637 chr19:55791153-55791160 chr19:55791777-55791786 chr19:55791794-55791806 chr19:55791226-55791238 chr19:55791227-55791237 chr19:55791795-55791805 chr19:55791126-55791140 chr19:55791606-55791616 chr19:55791795-55791805 chr19:55791795-55791804 chr19:55791871-55791883 chr19:55791606-55791615 chr19:55791777-55791787 chr19:55791871-55791883 chr19:55791627-55791636 chr19:55791776-55791788 chr19:55791729-55791741 chr19:55791605-55791617 chr19:55791626-55791640 chr19:55791776-55791788 chr19:55791607-55791616 chr19:55791626-55791635 chr19:55791794-55791806
7	YY1	chr19:55791077-55791739	A549	lung:	n/a	chr19:55791659-55791668 chr19:55791469-55791491 chr19:55791654-55791668 chr19:55791469-55791479 chr19:55791465-55791474 chr19:55791470-55791478
8	GABPA	chr19:55790888-55792063	MCF-7	breast:	n/a	chr19:55791796-55791805 chr19:55791657-55791666 chr19:55791778-55791787
9	TBL1XR1	chr19:55791017-55791637	GM12878	blood:	n/a	n/a
10	TCF12	chr19:55790901-55792322	A549	lung:	n/a	chr19:55791448-55791455
11	MXI1	chr19:55790853-55792025	IMR90	lung:	n/a	chr19:55791307-55791322 chr19:55791335-55791350 chr19:55791209-55791224
12	GTF2F1	chr19:55791039-55791727	Hela-S3	cervix:	n/a	n/a
13	JUN	chr19:55791041-55793083	K562	blood:	n/a	chr19:55792088-55792099
14	GABPA	chr19:55791036-55791848	MCF-7	breast:	n/a	chr19:55791796-55791805 chr19:55791657-55791666 chr19:55791778-55791787
15	YY1	chr19:55791057-55791685	H1-hESC	embryonic stem cell:	n/a	chr19:55791659-55791668 chr19:55791469-55791491 chr19:55791654-55791668 chr19:55791469-55791479 chr19:55791465-55791474 chr19:55791470-55791478
16	ZKSCAN1	chr19:55791022-55791710	Hela-S3	cervix:	n/a	n/a
17	YY1	chr19:55791013-55791764	SK-N-SH_RA	brain:	n/a	chr19:55791659-55791668 chr19:55791469-55791491 chr19:55791654-55791668 chr19:55791469-55791479 chr19:55791465-55791474 chr19:55791470-55791478
18	GABPA	chr19:55791071-55791893	HL-60	blood:	n/a	chr19:55791796-55791805 chr19:55791657-55791666 chr19:55791778-55791787
19	ZBTB7A	chr19:55790804-55792208	K562	blood:	n/a	chr19:55791646-55791653 chr19:55791665-55791672 chr19:55791103-55791114
20	SIN3AK20	chr19:55790897-55791738	PANC-1	pancreas:	n/a	n/a
21	GABPA	chr19:55790995-55792053	K562	blood:	n/a	chr19:55791796-55791805 chr19:55791657-55791666 chr19:55791778-55791787
22	REST	chr19:55790442-55791992	H1-neurons	neurons:	n/a	chr19:55791697-55791710 chr19:55791714-55791734 chr19:55791448-55791466
23	MAZ	chr19:55790665-55792640	IMR90	lung:	n/a	chr19:55792272-55792281 chr19:55790705-55790714 chr19:55792271-55792281 chr19:55792271-55792282 chr19:55792270-55792285 chr19:55792271-55792282 chr19:55791872-55791882
24	MTA3	chr19:55790912-55791758	GM12878	blood:	n/a	n/a
25	BCL3	chr19:55791033-55791736	A549	lung:	n/a	chr19:55791503-55791512 chr19:55791661-55791670
26	BHLHE40	chr19:55791008-55791773	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:55790757-55791760	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIX5	chr19:55790760-55792366	A549	lung:	n/a	chr19:55791808-55791817
29	RFX5	chr19:55791017-55791602	H1-hESC	embryonic stem cell:	n/a	chr19:55791212-55791227 chr19:55791241-55791250 chr19:55791311-55791325 chr19:55791238-55791253 chr19:55791284-55791298 chr19:55791341-55791350 chr19:55791286-55791300 chr19:55791213-55791227 chr19:55791215-55791224 chr19:55791336-55791351 chr19:55791336-55791351 chr19:55791335-55791352 chr19:55791339-55791353
30	ELF1	chr19:55790974-55791772	GM12878	blood:	n/a	chr19:55791477-55791490 chr19:55791479-55791490 chr19:55791502-55791511 chr19:55791501-55791512 chr19:55791501-55791512
31	YY1	chr19:55791076-55791756	SK-N-SH	brain:	n/a	chr19:55791659-55791668 chr19:55791469-55791491 chr19:55791654-55791668 chr19:55791469-55791479 chr19:55791465-55791474 chr19:55791470-55791478
32	GABPA	chr19:55791069-55791748	Hela-S3	cervix:	n/a	chr19:55791657-55791666
33	POLR2A	chr19:55791024-55791710	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr19:55791085-55791660	H1-hESC	embryonic stem cell:	n/a	chr19:55791129-55791139
35	YY1	chr19:55791028-55791726	GM12892	blood:	n/a	chr19:55791659-55791668 chr19:55791469-55791491 chr19:55791654-55791668 chr19:55791469-55791479 chr19:55791465-55791474 chr19:55791470-55791478
36	REST	chr19:55791082-55791796	A549	lung:	n/a	chr19:55791697-55791710 chr19:55791714-55791734 chr19:55791448-55791466
37	POLR2A	chr19:55791090-55791917	HepG2	liver:	n/a	n/a
38	ELK1	chr19:55791086-55791707	Hela-S3	cervix:	n/a	chr19:55791481-55791490 chr19:55791481-55791490
39	YY1	chr19:55790873-55791762	HepG2	liver:	n/a	chr19:55791659-55791668 chr19:55791469-55791491 chr19:55791654-55791668 chr19:55791469-55791479 chr19:55791465-55791474 chr19:55791470-55791478
40	HCFC1	chr19:55790314-55793324	Hela-S3	cervix:	n/a	n/a
41	TAF1	chr19:55791042-55791817	ECC-1	luminal epithelium:	n/a	n/a
42	SP1	chr19:55791077-55792014	H1-hESC	embryonic stem cell:	n/a	chr19:55791795-55791804 chr19:55791777-55791791 chr19:55791605-55791617 chr19:55791606-55791620 chr19:55791777-55791787 chr19:55791610-55791622 chr19:55791872-55791882 chr19:55791625-55791637 chr19:55791606-55791615 chr19:55791730-55791739 chr19:55791660-55791672 chr19:55791778-55791787 chr19:55791777-55791786 chr19:55791606-55791616 chr19:55791227-55791237 chr19:55791731-55791740 chr19:55791729-55791741 chr19:55791860-55791867 chr19:55791796-55791805 chr19:55791625-55791637 chr19:55791153-55791160 chr19:55791777-55791786 chr19:55791794-55791806 chr19:55791226-55791238 chr19:55791227-55791237 chr19:55791795-55791805 chr19:55791126-55791140 chr19:55791606-55791616 chr19:55791795-55791805 chr19:55791795-55791804 chr19:55791871-55791883 chr19:55791606-55791615 chr19:55791777-55791787 chr19:55791871-55791883 chr19:55791627-55791636 chr19:55791776-55791788 chr19:55791729-55791741 chr19:55791605-55791617 chr19:55791626-55791640 chr19:55791776-55791788 chr19:55791607-55791616 chr19:55791626-55791635 chr19:55791794-55791806
43	SIN3AK20	chr19:55791042-55791681	K562	blood:	n/a	n/a
44	SIN3AK20	chr19:55791033-55791595	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZEB1	chr19:55790989-55791883	GM12878	blood:	n/a	chr19:55791446-55791459 chr19:55791581-55791588 chr19:55791447-55791456
46	GABPA	chr19:55791003-55791954	HL-60	blood:	n/a	chr19:55791796-55791805 chr19:55791657-55791666 chr19:55791778-55791787
47	MTA3	chr19:55791079-55791650	GM12878	blood:	n/a	n/a
48	SIN3AK20	chr19:55791039-55791747	A549	lung:	n/a	n/a
49	POLR2A	chr19:55791091-55791758	GM12892	blood:	n/a	n/a
50	POLR2A	chr19:55790997-55792828	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55790334..55792779-chr19:55835222..55838188,2	K562	blood:
2	chr19:55764275..55774774-chr19:55790059..55800763,24	K562	blood:
3	chr19:55789007..55794976-chr19:55917716..55921043,9	K562	blood:
4	chr19:55788649..55794261-chr19:55847636..55852828,10	K562	blood:
5	chr19:55790067..55793851-chr19:55895113..55900809,14	K562	blood:
6	chr19:55789004..55791837-chr19:56110524..56113034,2	K562	blood:
7	chr19:55685149..55688070-chr19:55790255..55792658,4	K562	blood:
8	chr19:55790346..55793216-chr19:55794114..55797002,3	MCF-7	breast:
9	chr19:55789731..55792765-chr19:55910242..55912226,3	K562	blood:
10	chr19:55726686..55729337-chr19:55790310..55792413,2	MCF-7	breast:
11	chr19:55788570..55793941-chr19:55917523..55920740,5	MCF-7	breast:
12	chr19:55790016..55797764-chr19:55893451..55899813,15	MCF-7	breast:
13	chr19:55767441..55772178-chr19:55789060..55793175,7	MCF-7	breast:
14	chr19:55789812..55792675-chr19:55848548..55852419,5	K562	blood:
15	chr19:55787879..55795650-chr19:55893762..55898931,9	MCF-7	breast:
16	chr19:55725155..55730672-chr19:55787708..55794060,8	K562	blood:
17	chr19:55791017..55793325-chr19:55986469..55989325,2	MCF-7	breast:
18	chr19:55758319..55759930-chr19:55790512..55793308,2	MCF-7	breast:
19	chr19:55789007..55793013-chr19:55917737..55920988,5	K562	blood:
20	chr19:55790204..55793295-chr19:55914436..55917425,4	K562	blood:
21	chr19:55769028..55772088-chr19:55788931..55793273,6	MCF-7	breast:
22	chr19:55790075..55793363-chr19:55895323..55900809,10	K562	blood:
23	chr19:55790480..55793295-chr19:55915028..55917425,3	K562	blood:
24	chr19:55789771..55793296-chr19:55950803..55954133,4	K562	blood:
25	chr19:55727873..55730829-chr19:55787708..55791463,3	K562	blood:
26	chr19:55790045..55791863-chr19:55848758..55853021,3	MCF-7	breast:
27	chr19:55767517..55772398-chr19:55789828..55793738,15	K562	blood:

Variant related genes	Relation type
HSPBP1	TF binding region
BRSK1	TF binding region
ENSG00000197483	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000180061	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000187902	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000269859	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10403164	0.85[AMR][1000 genomes]
rs10403571	0.84[AMR][1000 genomes]
rs10412187	0.85[AMR][1000 genomes]
rs10414721	0.85[AMR][1000 genomes]
rs11880758	0.85[AMR][1000 genomes]
rs11880781	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12974813	0.92[ASN][1000 genomes]
rs12983085	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4072920	0.86[AMR][1000 genomes]
rs4473307	0.81[AMR][1000 genomes]
rs4806656	0.82[AMR][1000 genomes]
rs4806657	0.90[AMR][1000 genomes]
rs67351527	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr19:55771400-55791600	Weak transcription	Fetal Heart	heart
2	chr19:55790200-55792000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:55790200-55792000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:55790200-55792200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:55790400-55791200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:55790400-55791200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:55790400-55791200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:55790400-55791200	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr19:55790400-55791200	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr19:55790400-55791200	Flanking Active TSS	Fetal Brain Male	brain
11	chr19:55790400-55791200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr19:55790400-55791200	Flanking Active TSS	GM12878-XiMat	blood
13	chr19:55790400-55791200	Flanking Active TSS	HUVEC	blood vessel
14	chr19:55790400-55791400	Flanking Active TSS	Liver	Liver
15	chr19:55790400-55792000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr19:55790400-55792000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr19:55790400-55792000	Active TSS	Fetal Stomach	stomach
18	chr19:55790400-55792000	Active TSS	Rectal Smooth Muscle	rectum
19	chr19:55790400-55792000	Active TSS	A549	lung
20	chr19:55790400-55792200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:55790400-55792200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:55790400-55792200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:55790400-55792200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr19:55790400-55792200	Flanking Active TSS	Dnd41	blood
25	chr19:55790600-55791200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:55790600-55791200	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr19:55790600-55791200	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr19:55790600-55791200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:55790600-55791200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr19:55790600-55791200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr19:55790600-55791200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:55790600-55791200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:55790600-55791200	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr19:55790600-55791200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr19:55790600-55791200	Flanking Active TSS	Esophagus	oesophagus
36	chr19:55790600-55791200	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr19:55790600-55791200	Flanking Active TSS	Lung	lung
38	chr19:55790600-55791200	Flanking Active TSS	Pancreas	Pancrea
39	chr19:55790600-55791200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
40	chr19:55790600-55791200	Flanking Active TSS	Right Ventricle	heart
41	chr19:55790600-55791200	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr19:55790600-55791200	Flanking Active TSS	Stomach Mucosa	stomach
43	chr19:55790600-55791200	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr19:55790600-55791400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr19:55790600-55791400	Flanking Active TSS	Colonic Mucosa	Colon
46	chr19:55790600-55791400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr19:55790600-55791400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:55790600-55791600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr19:55790600-55791600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:55790600-55791600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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