Variant report

Variant	rs56103707
Chromosome Location	chr19:44304188-44304189
allele	A/G
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	STAT3	chr19:44303970-44304468	MCF10A-Er-Src	breast:	n/a	chr19:44304234-44304243 chr19:44304300-44304312 chr19:44304233-44304242 chr19:44304232-44304243
2	FOS	chr19:44304034-44304478	MCF10A-Er-Src	breast:	n/a	chr19:44304279-44304290
3	MAX	chr19:44303996-44304205	K562	blood:	n/a	n/a
4	FOS	chr19:44304094-44304450	HUVEC	blood vessel:	n/a	chr19:44304279-44304290
5	FOS	chr19:44304077-44304462	MCF10A-Er-Src	breast:	n/a	chr19:44304279-44304290
6	STAT3	chr19:44303981-44304471	MCF10A-Er-Src	breast:	n/a	chr19:44304234-44304243 chr19:44304300-44304312 chr19:44304233-44304242 chr19:44304232-44304243
7	POLR2A	chr19:44303890-44304304	HCT-116	colon:	n/a	n/a
8	MYC	chr19:44304075-44304330	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr19:44304074-44304343	HUVEC	blood vessel:	n/a	n/a
10	E2F4	chr19:44304088-44304364	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr19:44304022-44304360	MCF10A-Er-Src	breast:	n/a	chr19:44304234-44304243 chr19:44304300-44304312 chr19:44304233-44304242 chr19:44304232-44304243
12	STAT3	chr19:44303975-44304457	MCF10A-Er-Src	breast:	n/a	chr19:44304234-44304243 chr19:44304300-44304312 chr19:44304233-44304242 chr19:44304232-44304243
13	FOS	chr19:44304057-44304470	MCF10A-Er-Src	breast:	n/a	chr19:44304279-44304290

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
LYPD5	TF binding region
ENSG00000159871	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10401170	0.92[ASN][1000 genomes]
rs10401203	0.92[ASN][1000 genomes]
rs10426528	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs349045	0.86[ASN][1000 genomes]
rs349046	0.92[ASN][1000 genomes]
rs349047	0.92[ASN][1000 genomes]
rs349048	0.92[ASN][1000 genomes]
rs349049	0.95[ASN][1000 genomes]
rs349050	0.95[ASN][1000 genomes]
rs349053	0.95[ASN][1000 genomes]
rs349055	1.00[ASN][1000 genomes]
rs62116990	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62116991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104447	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111664	0.86[EUR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56103707	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx
rs56103707	LYPD5	cis	Skin Sun Exposed Lower leg	GTEx
rs56103707	KCNN4	cis	Whole Blood	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44302400-44304400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:44303000-44304200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr19:44303200-44304200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:44303200-44304200	Enhancers	Left Ventricle	heart
5	chr19:44303200-44304400	Enhancers	HUVEC	blood vessel
6	chr19:44303400-44304200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:44303400-44304200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:44303400-44304200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr19:44303400-44304200	Enhancers	Gastric	stomach
10	chr19:44303400-44304200	Enhancers	Stomach Mucosa	stomach
11	chr19:44303400-44304400	Enhancers	Hela-S3	cervix
12	chr19:44303400-44304600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:44303400-44304600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:44303400-44304600	Enhancers	Spleen	Spleen
15	chr19:44303400-44305000	Weak transcription	Right Atrium	heart
16	chr19:44303600-44304200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:44303600-44304200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:44303600-44304200	Enhancers	Lung	lung
19	chr19:44303600-44304400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr19:44303600-44304600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr19:44303800-44304200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr19:44303800-44304200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr19:44303800-44304400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr19:44303800-44304400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr19:44303800-44304600	Enhancers	Placenta	Placenta
26	chr19:44304000-44304200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
27	chr19:44304000-44304200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
28	chr19:44304000-44304200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:44304000-44304200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:44304000-44304200	Enhancers	Esophagus	oesophagus
31	chr19:44304000-44304200	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr19:44304000-44304200	Enhancers	K562	blood
33	chr19:44304000-44304400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
34	chr19:44304000-44304600	Enhancers	HMEC	breast
35	chr19:44304000-44304600	Enhancers	NHEK	skin

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