Variant report

Variant	rs349053
Chromosome Location	chr19:44302624-44302625
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	MAX	chr19:44302585-44303366	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:44302284-44303531	HCT-116	colon:	n/a	n/a
3	BCL3	chr19:44302339-44302760	A549	lung:	n/a	n/a
4	POLR2A	chr19:44302619-44303235	HCT-116	colon:	n/a	n/a
5	POLR2A	chr19:44302610-44303291	HCT-116	colon:	n/a	n/a
6	MAX	chr19:44302596-44303311	A549	lung:	n/a	n/a
7	MAX	chr19:44302527-44303306	ECC-1	luminal epithelium:	n/a	n/a
8	SIN3A	chr19:44302570-44303355	H1-hESC	embryonic stem cell:	n/a	chr19:44302948-44302959
9	HMGN3	chr19:44302600-44303134	K562	blood:	n/a	n/a
10	POLR2A	chr19:44302564-44303234	HCT-116	colon:	n/a	n/a
11	MAX	chr19:44302612-44303395	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr19:44302537-44303264	ECC-1	luminal epithelium:	n/a	n/a
13	ZNF263	chr19:44301624-44303510	HEK293-T-REx	kidney:	n/a	chr19:44303227-44303248
14	NFIC	chr19:44302584-44303199	ECC-1	luminal epithelium:	n/a	n/a
15	MTA3	chr19:44302425-44302751	GM12878	blood:	n/a	n/a
16	CHD2	chr19:44302587-44303272	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr19:44302558-44303431	H1-hESC	embryonic stem cell:	n/a	chr19:44302863-44302874 chr19:44302864-44302875 chr19:44302951-44302963 chr19:44302865-44302875
18	POLR2A	chr19:44302062-44302745	MCF-7	breast:	n/a	n/a
19	BRCA1	chr19:44302617-44302803	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr19:44302611-44303301	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44301885..44304341-chr19:44304382..44306763,2	K562	blood:

Variant related genes	Relation type
ENSG00000268601	TF binding region
ENSG00000159871	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10401170	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10401203	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10416177	0.84[AFR][1000 genomes]
rs10426528	0.97[ASN][1000 genomes]
rs11547806	0.86[AFR][1000 genomes]
rs349045	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs349046	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs349047	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs349048	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs349049	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs349050	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs349055	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56103707	0.95[ASN][1000 genomes]
rs62116990	1.00[ASN][1000 genomes]
rs62116991	0.95[ASN][1000 genomes]
rs73048670	0.81[ASN][1000 genomes]
rs8104447	0.97[ASN][1000 genomes]
rs8111664	0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs349053	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44302200-44302800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
2	chr19:44302200-44303200	Flanking Active TSS	GM12878-XiMat	blood
3	chr19:44302200-44303400	Active TSS	Brain Angular Gyrus	brain
4	chr19:44302200-44303400	Active TSS	Brain Anterior Caudate	brain
5	chr19:44302400-44302800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
6	chr19:44302400-44302800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:44302400-44302800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr19:44302400-44302800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
9	chr19:44302400-44302800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:44302400-44302800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
11	chr19:44302400-44302800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:44302400-44302800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr19:44302400-44302800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:44302400-44302800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
15	chr19:44302400-44302800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:44302400-44302800	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr19:44302400-44302800	Bivalent Enhancer	Fetal Thymus	thymus
18	chr19:44302400-44302800	Bivalent Enhancer	Left Ventricle	heart
19	chr19:44302400-44302800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr19:44302400-44302800	Flanking Active TSS	HMEC	breast
21	chr19:44302400-44302800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr19:44302400-44302800	Flanking Active TSS	NHEK	skin
23	chr19:44302400-44303000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:44302400-44303000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:44302400-44303000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr19:44302400-44303000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
27	chr19:44302400-44303000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr19:44302400-44303000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr19:44302400-44303000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr19:44302400-44303000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr19:44302400-44303000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
32	chr19:44302400-44303000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr19:44302400-44303000	Flanking Active TSS	Stomach Mucosa	stomach
34	chr19:44302400-44303200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:44302400-44303200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
36	chr19:44302400-44303200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr19:44302400-44303200	Active TSS	K562	blood
38	chr19:44302400-44303400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:44302400-44303400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:44302400-44303400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:44302400-44303400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:44302400-44303400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
43	chr19:44302400-44303400	Active TSS	Brain Cingulate Gyrus	brain
44	chr19:44302400-44303400	Flanking Active TSS	Colonic Mucosa	Colon
45	chr19:44302400-44303400	Flanking Active TSS	Spleen	Spleen
46	chr19:44302400-44303400	Active TSS	A549	lung
47	chr19:44302400-44303600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
48	chr19:44302400-44303600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
49	chr19:44302400-44303600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr19:44302400-44303600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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