Variant report

Variant	rs11549030
Chromosome Location	chr19:36246418-36246419
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:244)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36243424-36249712	IMR90	lung:	n/a	n/a
2	POLR2A	chr19:36246252-36246603	K562	blood:	n/a	n/a
3	MAZ	chr19:36245970-36249729	IMR90	lung:	n/a	chr19:36246654-36246663
4	POLR2A	chr19:36246089-36247182	ProgFib	skin:	n/a	n/a
5	POLR2A	chr19:36246245-36246740	HepG2	liver:	n/a	n/a
6	MXI1	chr19:36246145-36247840	IMR90	lung:	n/a	n/a
7	BACH1	chr19:36246283-36246801	H1-hESC	embryonic stem cell:	n/a	n/a

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:36246408-36246458	SAEC	small airway:	n/a
2	chr19:36246402-36246452	LNCaP	prostate:	n/a
3	chr19:36246395-36246445	NT2-D1	testis:	n/a
4	chr19:36246402-36246452	SKMC	muscle:	n/a
5	chr19:36246395-36246445	HAEpiC	amniotic membrane:	n/a
6	chr19:36246395-36246445	NHDF-neo	bronchial:	n/a
7	chr19:36246402-36246452	BE2_C	brain:	n/a
8	chr19:36246406-36246456	HCM	heart:	n/a
9	chr19:36246406-36246456	T-47D	breast:	n/a
10	chr19:36246395-36246445	PFSK-1	brain:	n/a
11	chr19:36246406-36246456	HRPEpiC	eye:	n/a
12	chr19:36246406-36246456	MCF10A-Er-Src	breast:	n/a
13	chr19:36246402-36246452	PFSK-1	brain:	n/a
14	chr19:36246395-36246445	BJ	skin:	n/a
15	chr19:36246408-36246458	AG09319	gingival:	n/a
16	chr19:36246395-36246445	Hela-S3	cervix:	n/a
17	chr19:36246395-36246445	SK-N-SH	brain:	n/a
18	chr19:36246406-36246456	AoSMC	blood vessel:	n/a
19	chr19:36246395-36246445	GM06990	blood:	n/a
20	chr19:36246406-36246456	NT2-D1	testis:	n/a
21	chr19:36246406-36246456	Hepatocyte	liver:	n/a
22	chr19:36246408-36246458	ovcar-3	ovarian:	n/a
23	chr19:36246395-36246445	CMK	blood:	n/a
24	chr19:36246402-36246452	GM12892	blood:	n/a
25	chr19:36246402-36246452	GM12878	blood:	n/a
26	chr19:36246395-36246445	GM12892	blood:	n/a
27	chr19:36246406-36246456	Jurkat	blood:	n/a
28	chr19:36246408-36246458	IMR90	lung:	fetal
29	chr19:36246406-36246456	ProgFib	skin:	n/a
30	chr19:36246408-36246458	HIPEpiC	eye:	n/a
31	chr19:36246402-36246452	GM06990	blood:	n/a
32	chr19:36246408-36246458	HRPEpiC	eye:	n/a
33	chr19:36246408-36246458	HNPCEpiC	eye:	n/a
34	chr19:36246395-36246445	Jurkat	blood:	n/a
35	chr19:36246406-36246456	GM19239	blood:	n/a
36	chr19:36246402-36246452	SAEC	small airway:	n/a
37	chr19:36246395-36246445	HEK293	kidney:	embryo
38	chr19:36246402-36246452	HRPEpiC	eye:	n/a
39	chr19:36246406-36246456	GM12878	blood:	n/a
40	chr19:36246408-36246458	GM12891	blood:	n/a
41	chr19:36246395-36246445	HRCEpiC	kidney:	n/a
42	chr19:36246406-36246456	A549	lung:	n/a
43	chr19:36246406-36246456	IMR90	lung:	fetal
44	chr19:36246402-36246452	HL-60	blood:	n/a
45	chr19:36246408-36246458	AG09309	skin:	n/a
46	chr19:36246408-36246458	MCF10A-Er-Src	breast:	n/a
47	chr19:36246402-36246452	PrEC	prostate:	n/a
48	chr19:36246408-36246458	GM12878	blood:	n/a
49	chr19:36246408-36246458	GM06990	blood:	n/a
50	chr19:36246408-36246458	HEEpiC	esophagus:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36245255..36250047-chr19:36263979..36267864,8	K562	blood:
2	chr19:36238866..36244880-chr19:36246037..36252437,21	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267439	TF binding region
C19orf55	TF binding region
C19orf55	CpG island
ENSG00000267439	CpG island
ENSG00000267796	Chromatin interaction
ENSG00000004777	Chromatin interaction
ENSG00000267439	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10401156	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402601	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402837	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12459634	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293686	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28656784	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871921	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3746277	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761087	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848662	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3848665	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62112162	0.86[EUR][1000 genomes]
rs7260184	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11549030	U2AF1L4	cis	lung	GTEx
rs11549030	LIN37	Cis_1M	lymphoblastoid	RTeQTL
rs11549030	U2AF1L4	cis	Esophagus Muscularis	GTEx
rs11549030	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs11549030	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs11549030	TMEM149	cis	multi-tissue	Pritchard
rs11549030	U2AF1L4	cis	Whole Blood	GTEx
rs11549030	U2AF1L4	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36240400-36247200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:36241000-36247600	Weak transcription	HMEC	breast
3	chr19:36241200-36247800	Weak transcription	Hela-S3	cervix
4	chr19:36242400-36247200	Strong transcription	A549	lung
5	chr19:36242600-36247000	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:36242600-36247200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:36243800-36247800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
8	chr19:36244600-36247600	Weak transcription	GM12878-XiMat	blood
9	chr19:36245200-36247800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:36245400-36247000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:36245400-36247600	Weak transcription	Dnd41	blood
12	chr19:36245600-36246600	Enhancers	Gastric	stomach
13	chr19:36245600-36246800	Enhancers	Fetal Heart	heart
14	chr19:36245600-36247000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:36245600-36247000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:36245600-36247200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:36245600-36247200	Weak transcription	Brain Anterior Caudate	brain
18	chr19:36245600-36247600	Weak transcription	Brain Angular Gyrus	brain
19	chr19:36245600-36247800	Weak transcription	Brain Substantia Nigra	brain
20	chr19:36245600-36247800	Weak transcription	HepG2	liver
21	chr19:36245600-36248000	Weak transcription	K562	blood
22	chr19:36245800-36246800	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:36245800-36247200	Flanking Active TSS	Fetal Lung	lung
24	chr19:36245800-36247600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:36245800-36248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:36246000-36246600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:36246000-36246800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr19:36246000-36247000	Bivalent Enhancer	Fetal Thymus	thymus
29	chr19:36246000-36247000	Enhancers	Lung	lung
30	chr19:36246000-36247000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr19:36246000-36247000	Enhancers	Small Intestine	intestine
32	chr19:36246000-36247200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:36246000-36247200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:36246000-36247200	Transcr. at gene 5' and 3'	NHLF	lung
35	chr19:36246000-36247400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr19:36246000-36248000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr19:36246000-36248000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr19:36246000-36248200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr19:36246000-36248400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr19:36246000-36248600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:36246000-36248600	Enhancers	Spleen	Spleen
42	chr19:36246000-36248800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:36246000-36248800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr19:36246000-36248800	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr19:36246000-36249800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr19:36246200-36246600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:36246200-36246600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:36246200-36246600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
49	chr19:36246200-36246600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr19:36246200-36246600	Flanking Active TSS	Colonic Mucosa	Colon

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