Variant report

Variant	rs4253238
Chromosome Location	chr4:187148387-187148388
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	FOXA2	chr4:187148050-187149060	HepG2	liver:	n/a	chr4:187149006-187149018
2	FOXA1	chr4:187148354-187148928	HepG2	liver:	n/a	chr4:187148623-187148638
3	NFIC	chr4:187148379-187148762	HepG2	liver:	n/a	chr4:187148610-187148626 chr4:187148610-187148627
4	FOXA1	chr4:187148312-187148801	HepG2	liver:	n/a	chr4:187148623-187148638
5	FOXA1	chr4:187148384-187148762	HepG2	liver:	n/a	chr4:187148623-187148638
6	CTCF	chr4:187148340-187148490	GM12869	blood:	n/a	n/a
7	MAFF	chr4:187148256-187148774	HepG2	liver:	n/a	n/a
8	MYBL2	chr4:187148285-187148786	HepG2	liver:	n/a	n/a
9	SP1	chr4:187148387-187148762	HepG2	liver:	n/a	n/a
10	EP300	chr4:187148360-187148797	HepG2	liver:	n/a	n/a
11	MBD4	chr4:187148374-187148738	HepG2	liver:	n/a	n/a
12	NFIC	chr4:187148348-187148875	HepG2	liver:	n/a	chr4:187148610-187148626 chr4:187148610-187148627

Variant related genes	Relation type
KLKB1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1053094	0.80[CHB][hapmap]
rs11132382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12331618	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1511801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912826	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973612	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35984397	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733402	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775298	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241815	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241816	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241817	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241818	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241819	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4253236	0.86[CHB][hapmap]
rs4253248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4253252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4253254	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4253255	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4253272	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4253281	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4253282	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4253311	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4862669	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66530140	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71640034	0.82[AMR][1000 genomes]
rs71640036	0.81[AMR][1000 genomes];0.86[EUR][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

Variant related diseases (count:1)

Disease	PMID	Source
Circulating vasoactive peptide levels	23381795	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4253238	F11	cis	parietal	SCAN
rs4253238	STOX2	cis	parietal	SCAN
rs4253238	F11	cis	cerebellum	SCAN
rs4253238	CYP4V2	cis	parietal	SCAN

Chromatin state (count:26 , 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	chr4:187131600-187148400	Weak transcription	Fetal Kidney	kidney
4	chr4:187131800-187149000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:187131800-187159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:187131800-187181600	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:187134000-187149000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:187146400-187172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:187147400-187148400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:187147400-187148600	ZNF genes & repeats	Fetal Intestine Small	intestine
11	chr4:187147600-187148400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:187147600-187148600	Flanking Active TSS	Liver	Liver
13	chr4:187147800-187148400	Enhancers	Pancreas	Pancrea
14	chr4:187147800-187148400	Enhancers	Right Ventricle	heart
15	chr4:187147800-187149000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:187147800-187149200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:187147800-187162000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:187148000-187149200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:187148000-187149400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:187148000-187161600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:187148000-187173000	Weak transcription	Psoas Muscle	Psoas
22	chr4:187148200-187148400	Enhancers	Ovary	ovary
23	chr4:187148200-187150200	Enhancers	Fetal Lung	lung
24	chr4:187148200-187150400	Enhancers	HepG2	liver
25	chr4:187148200-187159400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:187148200-187179200	Weak transcription	Lung	lung

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