Variant report

Variant	rs11672373
Chromosome Location	chr19:55791380-55791381
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	MAX	chr19:55791099-55791800	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr19:55791271-55791711	A549	lung:	n/a	chr19:55791448-55791455
5	E2F6	chr19:55791346-55792525	K562	blood:	n/a	chr19:55791627-55791636 chr19:55791778-55791787 chr19:55791657-55791667
6	ELF1	chr19:55791343-55791680	HepG2	liver:	n/a	chr19:55791477-55791490 chr19:55791479-55791490 chr19:55791502-55791511 chr19:55791501-55791512 chr19:55791501-55791512
7	FOSL2	chr19:55791267-55791659	A549	lung:	n/a	n/a
8	HA-E2F1	chr19:55791296-55791755	MCF-7	breast:	n/a	chr19:55791627-55791636 chr19:55791657-55791667
9	MYBL2	chr19:55791218-55791628	HepG2	liver:	n/a	n/a
10	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
11	EP300	chr19:55791285-55792871	K562	blood:	n/a	chr19:55791504-55791511 chr19:55791657-55791666
12	EP300	chr19:55790914-55791740	A549	lung:	n/a	chr19:55791504-55791511 chr19:55791657-55791666
13	POLR2A	chr19:55791068-55791787	U87	brain:	n/a	n/a
14	BHLHE40	chr19:55791246-55791762	GM12878	blood:	n/a	n/a
15	EP300	chr19:55791110-55791586	GM12878	blood:	n/a	chr19:55791504-55791511
16	RELA	chr19:55791173-55791659	GM18951	blood:	n/a	n/a
17	TBP	chr19:55791294-55791715	Hela-S3	cervix:	n/a	n/a
18	MAFK	chr19:55791369-55791569	HepG2	liver:	n/a	n/a
19	RCOR1	chr19:55791275-55791646	HepG2	liver:	n/a	n/a
20	CREB1	chr19:55791238-55791777	ECC-1	luminal epithelium:	n/a	n/a
21	MYC	chr19:55791239-55791738	MCF-7	breast:	n/a	n/a
22	BCLAF1	chr19:55791162-55791680	K562	blood:	n/a	chr19:55791503-55791512 chr19:55791661-55791670
23	E2F6	chr19:55791124-55792082	A549	lung:	n/a	chr19:55791627-55791636 chr19:55791778-55791787 chr19:55791657-55791667
24	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
25	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
26	POLR2A	chr19:55791187-55791700	HUVEC	blood vessel:	n/a	n/a
27	FOS	chr19:55791372-55791669	MCF10A-Er-Src	breast:	n/a	n/a
28	SMC3	chr19:55791193-55792186	Hela-S3	cervix:	n/a	chr19:55791780-55791790
29	GABPA	chr19:55790888-55792063	MCF-7	breast:	n/a	chr19:55791796-55791805 chr19:55791657-55791666 chr19:55791778-55791787
30	TBL1XR1	chr19:55791017-55791637	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:55791092-55791725	MCF-7	breast:	n/a	n/a
32	EP300	chr19:55791293-55791609	GM12878	blood:	n/a	chr19:55791504-55791511
33	MAX	chr19:55791095-55791787	H1-hESC	embryonic stem cell:	n/a	n/a
34	TCF12	chr19:55790901-55792322	A549	lung:	n/a	chr19:55791448-55791455
35	MXI1	chr19:55790853-55792025	IMR90	lung:	n/a	chr19:55791307-55791322 chr19:55791335-55791350 chr19:55791209-55791224
36	GTF2F1	chr19:55791039-55791727	Hela-S3	cervix:	n/a	n/a
37	SIN3AK20	chr19:55791099-55791636	A549	lung:	n/a	n/a
38	POLR2A	chr19:55791138-55791741	PANC-1	pancreas:	n/a	n/a
39	GTF2F1	chr19:55791369-55791641	H1-hESC	embryonic stem cell:	n/a	n/a
40	KAP1	chr19:55791315-55791645	U2OS	brain:	n/a	n/a
41	POLR2A	chr19:55791207-55791710	A549	lung:	n/a	n/a
42	FOXM1	chr19:55791100-55791805	GM12878	blood:	n/a	n/a
43	MYC	chr19:55791171-55791722	NB4	blood:	n/a	n/a
44	POLR2A	chr19:55791248-55791691	GM12892	blood:	n/a	n/a
45	YY1	chr19:55791112-55791764	K562	blood:	n/a	chr19:55791659-55791668 chr19:55791469-55791491 chr19:55791654-55791668 chr19:55791469-55791479 chr19:55791465-55791474 chr19:55791470-55791478
46	SIN3AK20	chr19:55791160-55791607	PFSK-1	brain:	n/a	n/a
47	JUN	chr19:55791041-55793083	K562	blood:	n/a	chr19:55792088-55792099
48	TBP	chr19:55791283-55791748	HepG2	liver:	n/a	n/a
49	ELF1	chr19:55791193-55791803	K562	blood:	n/a	chr19:55791477-55791490 chr19:55791479-55791490 chr19:55791502-55791511 chr19:55791501-55791512 chr19:55791501-55791512
50	GABPA	chr19:55791036-55791848	MCF-7	breast:	n/a	chr19:55791796-55791805 chr19:55791657-55791666 chr19:55791778-55791787

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
ENSG00000269859	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000180061	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000187902	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1042506	1.00[JPT][hapmap]
rs11665832	0.82[AFR][1000 genomes]
rs11672710	0.87[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs17700265	1.00[JPT][hapmap]
rs35159664	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3848608	0.92[GIH][hapmap]
rs3848610	0.87[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap]
rs4252567	1.00[JPT][hapmap]
rs4252568	1.00[JPT][hapmap]
rs4644955	0.84[GIH][hapmap]
rs4801603	1.00[JPT][hapmap]
rs4806652	0.88[GIH][hapmap]
rs62126348	0.82[AFR][1000 genomes]
rs62126357	0.81[EUR][1000 genomes]
rs6509938	1.00[CEU][hapmap];0.88[GIH][hapmap]
rs7507151	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv912459	chr19:55791380-55845386	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 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	chr19:55790400-55791400	Flanking Active TSS	Liver	Liver
6	chr19:55790400-55792000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr19:55790400-55792000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:55790400-55792000	Active TSS	Fetal Stomach	stomach
9	chr19:55790400-55792000	Active TSS	Rectal Smooth Muscle	rectum
10	chr19:55790400-55792000	Active TSS	A549	lung
11	chr19:55790400-55792200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:55790400-55792200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:55790400-55792200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:55790400-55792200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr19:55790400-55792200	Flanking Active TSS	Dnd41	blood
16	chr19:55790600-55791400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr19:55790600-55791400	Flanking Active TSS	Colonic Mucosa	Colon
18	chr19:55790600-55791400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr19:55790600-55791400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr19:55790600-55791600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr19:55790600-55791600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:55790600-55791600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:55790600-55791800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:55790600-55791800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:55790600-55792000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr19:55790600-55792000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:55790600-55792000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr19:55790600-55792000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:55790600-55792000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr19:55790600-55792000	Active TSS	NHLF	lung
31	chr19:55790600-55792200	Active TSS	Fetal Kidney	kidney
32	chr19:55790600-55792400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:55790800-55791400	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr19:55790800-55791600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr19:55790800-55791600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:55790800-55791600	Active TSS	NHDF-Ad	bronchial
37	chr19:55790800-55791800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:55790800-55791800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:55790800-55791800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:55790800-55791800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:55790800-55791800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:55790800-55791800	Active TSS	Brain Angular Gyrus	brain
43	chr19:55790800-55791800	Active TSS	Fetal Intestine Large	intestine
44	chr19:55790800-55791800	Active TSS	Fetal Intestine Small	intestine
45	chr19:55790800-55791800	Active TSS	Hela-S3	cervix
46	chr19:55790800-55791800	Active TSS	HSMMtube	muscle
47	chr19:55790800-55791800	Active TSS	NHEK	skin
48	chr19:55790800-55792000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:55790800-55792000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:55790800-55792000	Active TSS	Ovary	ovary

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