Variant report

Variant	rs4253239
Chromosome Location	chr4:187148475-187148476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr4:187148050-187149060	HepG2	liver:	n/a	chr4:187149006-187149018
2	FOXA1	chr4:187148438-187148730	T-47D	breast:	n/a	chr4:187148623-187148638
3	FOXA2	chr4:187148418-187148730	HepG2	liver:	n/a	n/a
4	FOXA1	chr4:187148354-187148928	HepG2	liver:	n/a	chr4:187148623-187148638
5	FOXA1	chr4:187148464-187148742	T-47D	breast:	n/a	chr4:187148623-187148638
6	NFIC	chr4:187148379-187148762	HepG2	liver:	n/a	chr4:187148610-187148626 chr4:187148610-187148627
7	FOXA1	chr4:187148312-187148801	HepG2	liver:	n/a	chr4:187148623-187148638
8	FOXA1	chr4:187148384-187148762	HepG2	liver:	n/a	chr4:187148623-187148638
9	MAFK	chr4:187148390-187148780	HepG2	liver:	n/a	n/a
10	FOXA2	chr4:187148411-187148749	A549	lung:	n/a	n/a
11	CTCF	chr4:187148340-187148490	GM12869	blood:	n/a	n/a
12	MAFF	chr4:187148256-187148774	HepG2	liver:	n/a	n/a
13	MYBL2	chr4:187148285-187148786	HepG2	liver:	n/a	n/a
14	SP1	chr4:187148387-187148762	HepG2	liver:	n/a	n/a
15	EP300	chr4:187148360-187148797	HepG2	liver:	n/a	n/a
16	MBD4	chr4:187148374-187148738	HepG2	liver:	n/a	n/a
17	TCF12	chr4:187148475-187148723	HepG2	liver:	n/a	n/a
18	MAFK	chr4:187148388-187148773	HepG2	liver:	n/a	n/a
19	ARID3A	chr4:187148465-187148703	HepG2	liver:	n/a	n/a
20	FOXA1	chr4:187148417-187148806	HepG2	liver:	n/a	chr4:187148623-187148638
21	KAP1	chr4:187148388-187148700	U2OS	brain:	n/a	n/a
22	NFIC	chr4:187148348-187148875	HepG2	liver:	n/a	chr4:187148610-187148626 chr4:187148610-187148627

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:187148430-187148480	HCPEpiC	choroid plexus:	n/a
2	chr4:187148430-187148480	HAEpiC	amniotic membrane:	n/a
3	chr4:187148430-187148480	GM12878	blood:	n/a
4	chr4:187148430-187148480	HMEC	breast:	n/a
5	chr4:187148430-187148480	NH-A	brain:	n/a
6	chr4:187148430-187148480	SK-N-MC	brain:	n/a
7	chr4:187148430-187148480	HEEpiC	esophagus:	n/a
8	chr4:187148430-187148480	HRE	kidney:	n/a
9	chr4:187148430-187148480	SK-N-SH	brain:	n/a
10	chr4:187148430-187148480	AG04449	skin:	fetal
11	chr4:187148430-187148480	GM12891	blood:	n/a
12	chr4:187148430-187148480	ECC-1	luminal epithelium:	n/a
13	chr4:187148430-187148480	U87	brain:	n/a
14	chr4:187148430-187148480	HIPEpiC	eye:	n/a
15	chr4:187148430-187148480	AG09319	gingival:	n/a
16	chr4:187148430-187148480	HRPEpiC	eye:	n/a
17	chr4:187148430-187148480	PrEC	prostate:	n/a
18	chr4:187148430-187148480	HCF	heart:	n/a
19	chr4:187148430-187148480	PFSK-1	brain:	n/a
20	chr4:187148430-187148480	GM12892	blood:	n/a
21	chr4:187148430-187148480	Jurkat	blood:	n/a
22	chr4:187148430-187148480	HCT-116	colon:	n/a
23	chr4:187148430-187148480	ovcar-3	ovarian:	n/a
24	chr4:187148430-187148480	LNCaP	prostate:	n/a
25	chr4:187148430-187148480	HEK293	kidney:	embryo
26	chr4:187148430-187148480	GM19239	blood:	n/a
27	chr4:187148430-187148480	MCF-7	breast:	n/a
28	chr4:187148430-187148480	HRCEpiC	kidney:	n/a
29	chr4:187148430-187148480	Hela-S3	cervix:	n/a
30	chr4:187148430-187148480	BE2_C	brain:	n/a
31	chr4:187148430-187148480	HCM	heart:	n/a
32	chr4:187148430-187148480	MCF10A-Er-Src	breast:	n/a
33	chr4:187148430-187148480	HUVEC	blood vessel:	n/a
34	chr4:187148430-187148480	SK-N-SH_RA	brain:	n/a
35	chr4:187148430-187148480	T-47D	breast:	n/a
36	chr4:187148430-187148480	AG10803	skin:	n/a
37	chr4:187148430-187148480	AoSMC	blood vessel:	n/a
38	chr4:187148430-187148480	A549	lung:	n/a
39	chr4:187148430-187148480	Hepatocyte	liver:	n/a
40	chr4:187148430-187148480	NT2-D1	testis:	n/a
41	chr4:187148430-187148480	H1-hESC	embryonic stem cell:	embryo
42	chr4:187148430-187148480	HL-60	blood:	n/a
43	chr4:187148430-187148480	HNPCEpiC	eye:	n/a
44	chr4:187148430-187148480	HPAEpiC	pulmonary alveolar:	n/a
45	chr4:187148430-187148480	Caco-2	colon:	n/a
46	chr4:187148430-187148480	HepG2	liver:	n/a
47	chr4:187148430-187148480	AG04450	lung:	fetal
48	chr4:187148430-187148480	IMR90	lung:	fetal
49	chr4:187148430-187148480	NB4	blood:	n/a
50	chr4:187148430-187148480	ProgFib	skin:	n/a

No data

Variant related genes	Relation type
KLKB1	TF binding region
KLKB1	CpG island

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2304596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28721981	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4253260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4253262	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4253285	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4253292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4253302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4253318	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4253319	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4253321	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4253323	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4253330	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55686332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55846148	0.90[EUR][1000 genomes]
rs55975907	0.90[EUR][1000 genomes]
rs56105926	0.90[EUR][1000 genomes]
rs56413992	0.92[EUR][1000 genomes]
rs62348795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72710572	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9998455	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
3	nsv931977	chr4:186912987-187364756	Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv869299	chr4:186958290-187192748	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1033203	chr4:186990348-187333476	Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv537431	chr4:186990348-187333476	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv461864	chr4:187006806-187257004	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv596392	chr4:187006806-187257004	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv830172	chr4:187012765-187168424	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv461865	chr4:187072383-187366649	Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv596401	chr4:187072383-187366649	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv1023019	chr4:187082701-187153933	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv1022059	chr4:187082701-187183953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv881231	chr4:187136307-187157458	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4253239	STOX2	cis	parietal	SCAN
rs4253239	KLKB1	cis	cerebellum	SCAN
rs4253239	CYP4V2	cis	parietal	SCAN
rs4253239	KLKB1	cis	parietal	SCAN
rs4253239	CYP4V2	cis	cerebellum	SCAN
rs4253239	CYP4V2	Cis_1M	lymphoblastoid	RTeQTL
rs4253239	KLKB1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187125800-187149200	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:187130600-187149400	Weak transcription	Gastric	stomach
3	chr4:187131800-187149000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:187131800-187159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:187131800-187181600	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:187134000-187149000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:187146400-187172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:187147400-187148600	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr4:187147600-187148600	Flanking Active TSS	Liver	Liver
10	chr4:187147800-187149000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:187147800-187149200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:187147800-187162000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:187148000-187149200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:187148000-187149400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:187148000-187161600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:187148000-187173000	Weak transcription	Psoas Muscle	Psoas
17	chr4:187148200-187150200	Enhancers	Fetal Lung	lung
18	chr4:187148200-187150400	Enhancers	HepG2	liver
19	chr4:187148200-187159400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:187148200-187179200	Weak transcription	Lung	lung
21	chr4:187148400-187149000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr4:187148400-187149400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:187148400-187149400	Enhancers	Fetal Kidney	kidney
24	chr4:187148400-187149400	Weak transcription	Ovary	ovary
25	chr4:187148400-187162000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:187148400-187164600	Weak transcription	Right Ventricle	heart
27	chr4:187148400-187172600	Weak transcription	Brain Anterior Caudate	brain
28	chr4:187148400-187179400	Weak transcription	Pancreas	Pancrea

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