Variant report

Variant	rs2041220
Chromosome Location	chr19:38826184-38826185
allele	A/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	CTCF	chr19:38826183-38826460	MCF-7	breast:	n/a	chr19:38826291-38826309
2	CTCF	chr19:38826117-38826469	Lung_OC	lung:	n/a	chr19:38826291-38826309
3	CTCF	chr19:38826180-38826330	GM12866	blood:	n/a	chr19:38826291-38826309
4	CTCF	chr19:38826048-38826735	HCT-116	colon:	n/a	chr19:38826291-38826309
5	POU2F2	chr19:38826155-38826521	GM12891	blood:	n/a	n/a
6	YY1	chr19:38826095-38828043	A549	lung:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448 chr19:38827480-38827489
7	YY1	chr19:38826134-38826650	SK-N-SH_RA	brain:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448
8	CTCF	chr19:38825440-38827183	A549	lung:	n/a	chr19:38826291-38826309 chr19:38826985-38826995
9	CTCF	chr19:38826168-38826476	GM19239	blood:	n/a	chr19:38826291-38826309
10	CTCF	chr19:38826178-38826471	MCF-7	breast:	n/a	chr19:38826291-38826309
11	MYC	chr19:38826160-38826581	MCF10A-Er-Src	breast:	n/a	chr19:38826380-38826387 chr19:38826313-38826323
12	JUND	chr19:38826121-38826646	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr19:38825942-38827717	PANC-1	pancreas:	n/a	n/a
14	CTCF	chr19:38826158-38826494	GM12892	blood:	n/a	chr19:38826291-38826309
15	MAX	chr19:38826010-38828085	A549	lung:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
16	USF1	chr19:38826182-38826645	K562	blood:	n/a	n/a
17	CTCF	chr19:38826180-38826330	HA-sp	spinal cord:	n/a	chr19:38826291-38826309
18	RAD21	chr19:38825911-38827976	HCT-116	colon:	n/a	chr19:38826289-38826308 chr19:38826986-38826996 chr19:38826985-38826994
19	RAD21	chr19:38826078-38826439	GM12878	blood:	n/a	chr19:38826289-38826308
20	MAX	chr19:38826165-38827994	NB4	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
21	SMC3	chr19:38826084-38826503	GM12878	blood:	n/a	n/a
22	CTCF	chr19:38826181-38826462	LNCaP	prostate:	n/a	chr19:38826291-38826309
23	MAX	chr19:38826144-38827956	SK-N-SH	brain:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
24	EP300	chr19:38826161-38827269	K562	blood:	n/a	n/a
25	CTCF	chr19:38826177-38826493	HepG2	liver:	n/a	chr19:38826291-38826309
26	MYC	chr19:38826177-38826565	K562	blood:	n/a	chr19:38826380-38826387 chr19:38826313-38826323
27	CTCF	chr19:38826180-38826330	HCM	heart:	n/a	chr19:38826291-38826309
28	RAD21	chr19:38826103-38826496	A549	lung:	n/a	chr19:38826289-38826308
29	FOS	chr19:38826174-38826502	MCF10A-Er-Src	breast:	n/a	n/a
30	MAX	chr19:38826177-38826548	Hela-S3	cervix:	n/a	chr19:38826380-38826387 chr19:38826313-38826323
31	CREB1	chr19:38826166-38826524	A549	lung:	n/a	n/a
32	GABPA	chr19:38826078-38826665	A549	lung:	n/a	chr19:38826312-38826321
33	CTCF	chr19:38826090-38826502	K562	blood:	n/a	chr19:38826291-38826309
34	MYBL2	chr19:38826068-38826540	HepG2	liver:	n/a	n/a
35	SIX5	chr19:38826163-38826616	A549	lung:	n/a	n/a
36	MAZ	chr19:38826145-38828113	K562	blood:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
37	CTCF	chr19:38826177-38826464	Gliobla	brain:	n/a	chr19:38826291-38826309
38	MAZ	chr19:38826062-38828017	IMR90	lung:	n/a	chr19:38827422-38827432 chr19:38826380-38826387 chr19:38827478-38827488 chr19:38826313-38826323
39	ZKSCAN1	chr19:38826158-38826543	Hela-S3	cervix:	n/a	n/a
40	ATF3	chr19:38826139-38826521	K562	blood:	n/a	chr19:38826312-38826321 chr19:38826358-38826372
41	CTCF	chr19:38826157-38826480	GM19238	blood:	n/a	chr19:38826291-38826309
42	CTCF	chr19:38826180-38826330	GM12865	blood:	n/a	chr19:38826291-38826309
43	RAD21	chr19:38826012-38826517	K562	blood:	n/a	chr19:38826289-38826308
44	POLR2A	chr19:38826169-38827785	PANC-1	pancreas:	n/a	n/a
45	SP4	chr19:38826059-38826632	H1-hESC	embryonic stem cell:	n/a	chr19:38826308-38826324
46	ZEB1	chr19:38826184-38827693	GM12878	blood:	n/a	n/a
47	CREB1	chr19:38826051-38827921	GM12878	blood:	n/a	n/a
48	YY1	chr19:38826106-38827240	GM12878	blood:	n/a	chr19:38826437-38826447 chr19:38826437-38826459 chr19:38826435-38826452 chr19:38826436-38826452 chr19:38826440-38826448 chr19:38826436-38826448
49	CREB1	chr19:38826154-38826703	HepG2	liver:	n/a	n/a
50	CTCF	chr19:38825991-38826571	K562	blood:	n/a	chr19:38826291-38826309

No.	Distal block	Cell Line	Cell type
1	chr19:38804679..38808674-chr19:38824887..38827856,7	K562	blood:
2	chr19:38715608..38719883-chr19:38825304..38828918,6	K562	blood:
3	chr19:38720388..38721001-chr19:38825841..38826415,2	K562	blood:
4	chr19:38824766..38830853-chr19:38863348..38868089,16	MCF-7	breast:
5	chr19:38825004..38828693-chr19:38863595..38867873,9	K562	blood:
6	chr19:38823410..38828693-chr19:38863569..38867873,9	K562	blood:
7	chr19:38734151..38735191-chr19:38825824..38826459,3	K562	blood:
8	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
9	chr19:38825537..38827989-chr19:38835886..38838412,2	K562	blood:
10	chr19:38753791..38756428-chr19:38824915..38829046,7	MCF-7	breast:
11	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
12	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
13	chr19:38825745..38829204-chr19:38906597..38909224,3	K562	blood:
14	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
15	chr19:38733321..38734847-chr19:38824832..38827411,2	MCF-7	breast:
16	chr19:38733984..38735573-chr19:38825634..38828607,2	K562	blood:
17	chr19:38741131..38744022-chr19:38825237..38827049,2	K562	blood:
18	chr19:38746246..38748291-chr19:38825736..38828521,3	K562	blood:
19	chr19:38819188..38821432-chr19:38824241..38826346,2	K562	blood:
20	chr19:38806332..38809400-chr19:38825014..38828541,5	K562	blood:
21	chr19:38712277..38715341-chr19:38824721..38827828,3	K562	blood:
22	chr19:38777648..38780643-chr19:38825334..38827865,2	K562	blood:
23	chr19:38745286..38748830-chr19:38824490..38828580,5	K562	blood:
24	chr19:38733182..38735640-chr19:38825420..38827758,3	K562	blood:
25	chr19:38825387..38828116-chr19:38877119..38879831,3	MCF-7	breast:
26	chr19:38810007..38812286-chr19:38825422..38828123,4	MCF-7	breast:
27	chr19:38734193..38735131-chr19:38825868..38826446,2	MCF-7	breast:
28	chr19:38825542..38827860-chr19:38892803..38895034,2	K562	blood:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000179168	Chromatin interaction
ENSG00000267748	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000099337	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11672793	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2041220	C19orf33	cis	Heart Left Ventricle	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38811200-38826200	Weak transcription	Brain Anterior Caudate	brain
2	chr19:38811200-38826600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:38812000-38826600	Weak transcription	HUVEC	blood vessel
4	chr19:38812200-38826400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:38812200-38826600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:38812400-38826400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:38812400-38826400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr19:38812400-38826400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:38812600-38826200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:38813000-38826400	Weak transcription	Stomach Mucosa	stomach
11	chr19:38813200-38826800	Weak transcription	Fetal Heart	heart
12	chr19:38814000-38826400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr19:38814200-38826400	Weak transcription	Right Atrium	heart
14	chr19:38814600-38826400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:38815000-38826400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:38818000-38826600	Weak transcription	Small Intestine	intestine
17	chr19:38818200-38826600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:38818400-38826200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:38818400-38826600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:38818600-38826200	Weak transcription	Thymus	Thymus
21	chr19:38818600-38826400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:38818600-38826600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr19:38818800-38826400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:38818800-38826400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:38818800-38826400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:38818800-38826400	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:38818800-38826600	Weak transcription	Fetal Lung	lung
28	chr19:38819000-38826400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:38819000-38826400	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:38819000-38826600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:38819000-38826600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:38819000-38826600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:38819200-38826200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:38819200-38826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:38819200-38826400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:38819200-38826400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr19:38819200-38826400	Weak transcription	Colonic Mucosa	Colon
38	chr19:38819200-38826400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr19:38819200-38826400	Weak transcription	Fetal Intestine Small	intestine
40	chr19:38819200-38826400	Weak transcription	Left Ventricle	heart
41	chr19:38819200-38826400	Weak transcription	HMEC	breast
42	chr19:38819200-38826600	Weak transcription	Primary T cells from cord blood	blood
43	chr19:38819200-38826600	Weak transcription	Liver	Liver
44	chr19:38819200-38826600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr19:38819400-38826400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:38819400-38826400	Weak transcription	Primary B cells from cord blood	blood
47	chr19:38819400-38826400	Weak transcription	Adipose Nuclei	Adipose
48	chr19:38819400-38826400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:38819400-38826400	Weak transcription	Fetal Stomach	stomach
50	chr19:38819400-38826600	Weak transcription	Muscle Satellite Cultured Cells	--

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