Variant report

Variant	rs2569454
Chromosome Location	chr19:51523203-51523204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51521912-51523512	HCT-116	colon:	n/a	n/a
2	BCL3	chr19:51523027-51523420	A549	lung:	n/a	n/a
3	BCL3	chr19:51522896-51523535	A549	lung:	n/a	n/a
4	POLR2A	chr19:51521885-51523853	HCT-116	colon:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:51523159-51523209	PrEC	prostate:	n/a
2	chr19:51523159-51523209	HCF	heart:	n/a
3	chr19:51523159-51523209	NH-A	brain:	n/a
4	chr19:51523159-51523209	MCF10A-Er-Src	breast:	n/a
5	chr19:51523159-51523209	T-47D	breast:	n/a
6	chr19:51523159-51523209	SAEC	small airway:	n/a
7	chr19:51523159-51523209	Caco-2	colon:	n/a
8	chr19:51523159-51523209	NHBE	bronchial:	n/a
9	chr19:51523159-51523209	HEEpiC	esophagus:	n/a
10	chr19:51523159-51523209	U87	brain:	n/a
11	chr19:51523159-51523209	NHDF-neo	bronchial:	n/a
12	chr19:51523159-51523209	AG04449	skin:	fetal
13	chr19:51523159-51523209	SK-N-SH_RA	brain:	n/a
14	chr19:51523159-51523209	AG09319	gingival:	n/a
15	chr19:51523159-51523209	AG09309	skin:	n/a
16	chr19:51523159-51523209	Hepatocyte	liver:	n/a
17	chr19:51523159-51523209	HepG2	liver:	n/a
18	chr19:51523159-51523209	LNCaP	prostate:	n/a
19	chr19:51523159-51523209	AoSMC	blood vessel:	n/a
20	chr19:51523159-51523209	HUVEC	blood vessel:	n/a
21	chr19:51523159-51523209	BE2_C	brain:	n/a
22	chr19:51523159-51523209	GM06990	blood:	n/a
23	chr19:51523159-51523209	HL-60	blood:	n/a
24	chr19:51523159-51523209	RPTEC	kidney:	n/a
25	chr19:51523159-51523209	A549	lung:	n/a
26	chr19:51523159-51523209	H1-hESC	embryonic stem cell:	embryo
27	chr19:51523159-51523209	BJ	skin:	n/a
28	chr19:51523159-51523209	GM19239	blood:	n/a
29	chr19:51523159-51523209	HCM	heart:	n/a
30	chr19:51523159-51523209	ovcar-3	ovarian:	n/a
31	chr19:51523159-51523209	GM12878	blood:	n/a
32	chr19:51523159-51523209	NT2-D1	testis:	n/a
33	chr19:51523159-51523209	NB4	blood:	n/a
34	chr19:51523159-51523209	HEK293	kidney:	embryo
35	chr19:51523159-51523209	IMR90	lung:	fetal
36	chr19:51523159-51523209	HCT-116	colon:	n/a
37	chr19:51523159-51523209	ECC-1	luminal epithelium:	n/a
38	chr19:51523159-51523209	CMK	blood:	n/a
39	chr19:51523159-51523209	HRPEpiC	eye:	n/a
40	chr19:51523159-51523209	GM12892	blood:	n/a
41	chr19:51523159-51523209	PANC-1	pancreas:	n/a
42	chr19:51523159-51523209	AG10803	skin:	n/a
43	chr19:51523159-51523209	HMEC	breast:	n/a
44	chr19:51523159-51523209	K562	blood:	n/a
45	chr19:51523159-51523209	SK-N-MC	brain:	n/a
46	chr19:51523159-51523209	HRCEpiC	kidney:	n/a
47	chr19:51523159-51523209	ProgFib	skin:	n/a
48	chr19:51523159-51523209	HPAEpiC	pulmonary alveolar:	n/a
49	chr19:51523159-51523209	HIPEpiC	eye:	n/a
50	chr19:51523159-51523209	SK-N-SH	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:51517770..51520731-chr19:51521022..51523368,3	MCF-7	breast:
2	chr19:51306795..51309015-chr19:51522024..51524887,2	K562	blood:

No data

Variant related genes	Relation type
KLK10	TF binding region
KLK10	CpG island
ENSG00000167747	Chromatin interaction
ENSG00000129451	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2075688	0.89[ASN][1000 genomes]
rs3745535	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3760738	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];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	nsv912291	chr19:51505725-51537682	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2569454	KLK10	cis	Skin Sun Exposed Lower leg	GTEx
rs2569454	CTC-518B2.12	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51520000-51523400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr19:51520200-51523400	Active TSS	Ovary	ovary
3	chr19:51520400-51523600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:51520800-51523400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:51522000-51523400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr19:51522000-51523400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
7	chr19:51522000-51523600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr19:51522000-51524400	Bivalent Enhancer	Fetal Stomach	stomach
9	chr19:51522200-51523800	Bivalent Enhancer	Placenta	Placenta
10	chr19:51522200-51523800	Enhancers	Lung	lung
11	chr19:51522400-51523400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr19:51522400-51523400	Flanking Active TSS	HMEC	breast
13	chr19:51522400-51523400	Flanking Active TSS	NHEK	skin
14	chr19:51522400-51523600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:51522400-51524000	Enhancers	Brain Substantia Nigra	brain
16	chr19:51522600-51523400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
17	chr19:51522600-51523600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:51522600-51523800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr19:51522600-51525800	Weak transcription	Gastric	stomach
20	chr19:51522800-51523400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:51522800-51523400	Bivalent Enhancer	Adipose Nuclei	Adipose
22	chr19:51522800-51523400	Bivalent Enhancer	Brain Hippocampus Middle	brain
23	chr19:51522800-51523400	Bivalent Enhancer	Colonic Mucosa	Colon
24	chr19:51522800-51523400	Enhancers	Right Atrium	heart
25	chr19:51522800-51523400	Bivalent Enhancer	A549	lung
26	chr19:51522800-51523800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:51522800-51523800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
28	chr19:51523000-51523400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
29	chr19:51523000-51523400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr19:51523000-51523400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:51523000-51523400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:51523000-51523400	Weak transcription	Pancreas	Pancrea
33	chr19:51523000-51523600	Enhancers	Right Ventricle	heart
34	chr19:51523000-51523800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:51523000-51524200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr19:51523000-51524400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr19:51523000-51524600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:51523000-51524800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:51523000-51524800	Enhancers	Brain Anterior Caudate	brain
40	chr19:51523200-51523400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
41	chr19:51523200-51523400	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr19:51523200-51523400	Enhancers	Brain Cingulate Gyrus	brain
43	chr19:51523200-51523400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:51523200-51523400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr19:51523200-51523400	Flanking Active TSS	Esophagus	oesophagus
46	chr19:51523200-51523400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
47	chr19:51523200-51523400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
48	chr19:51523200-51523400	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
49	chr19:51523200-51523400	Bivalent Enhancer	HSMMtube	muscle
50	chr19:51523200-51524000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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