Variant report

Variant	rs4253299
Chromosome Location	chr4:187171355-187171356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr4:187171036-187171885	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:187171304-187171729	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr4:187171284-187171770	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr4:187171098-187171727	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr4:187171105-187171930	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr4:187171067-187171771	H1-hESC	embryonic stem cell:	n/a	chr4:187171133-187171144
7	POLR2A	chr4:187171309-187171747	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:187171042-187172034	H1-hESC	embryonic stem cell:	n/a	n/a
9	NANOG	chr4:187171266-187171705	H1-hESC	embryonic stem cell:	n/a	n/a
10	BACH1	chr4:187171005-187171725	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF143	chr4:187171136-187171789	H1-hESC	embryonic stem cell:	n/a	n/a
12	EP300	chr4:187171196-187171839	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr4:187171193-187171783	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF12	chr4:187171256-187171902	H1-hESC	embryonic stem cell:	n/a	n/a
15	GTF2F1	chr4:187171301-187171823	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr4:187171023-187172078	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD2	chr4:187171071-187172043	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr4:187171234-187171769	H1-hESC	embryonic stem cell:	n/a	n/a
19	CEBPB	chr4:187170950-187171465	IMR90	lung:	n/a	chr4:187171133-187171144
20	POU5F1	chr4:187171297-187171793	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD1	chr4:187171070-187171475	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAFK	chr4:187170491-187172006	H1-hESC	embryonic stem cell:	n/a	n/a
23	ATF2	chr4:187171143-187171925	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr4:187171321-187171803	H1-hESC	embryonic stem cell:	n/a	n/a
25	ATF2	chr4:187171045-187171934	H1-hESC	embryonic stem cell:	n/a	n/a
26	SP1	chr4:187171000-187172102	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF12	chr4:187171282-187171820	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF7	chr4:187170961-187172138	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr4:187170886-187172318	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBP	chr4:187170990-187171917	H1-hESC	embryonic stem cell:	n/a	n/a
31	TEAD4	chr4:187171329-187171763	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:187111874..187113781-chr4:187171263..187172793,2	MCF-7	breast:

No data

Variant related genes	Relation type
KLKB1	TF binding region
ENSG00000145476	Chromatin interaction
ENSG00000269302	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10014399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025990	0.89[ASN][1000 genomes]
rs2137145	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2175494	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221843	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380417	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3087505	1.00[CHD][hapmap]
rs3822055	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4241821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4253251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253274	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4253277	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253288	0.91[ASN][1000 genomes]
rs4253326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4862670	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
10	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
11	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
12	nsv881472	chr4:187152142-187187005	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4253299	F11	cis	parietal	SCAN
rs4253299	F11	cis	cerebellum	SCAN
rs4253299	LRP2BP	cis	cerebellum	SCAN
rs4253299	KLKB1	cis	Whole Blood	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187131800-187181600	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:187146400-187172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:187148000-187173000	Weak transcription	Psoas Muscle	Psoas
4	chr4:187148200-187179200	Weak transcription	Lung	lung
5	chr4:187148400-187172600	Weak transcription	Brain Anterior Caudate	brain
6	chr4:187148400-187179400	Weak transcription	Pancreas	Pancrea
7	chr4:187149800-187181600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:187149800-187186800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:187150200-187187200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:187151000-187187200	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:187151800-187173000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:187152000-187179400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:187154000-187182000	Weak transcription	Primary T cells from cord blood	blood
14	chr4:187156800-187179200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:187158000-187173000	Weak transcription	Left Ventricle	heart
16	chr4:187158400-187181400	Weak transcription	Fetal Intestine Large	intestine
17	chr4:187159800-187172600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:187168600-187173000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:187168600-187173000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:187169200-187173600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:187169400-187172400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr4:187169600-187171400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:187169600-187172000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:187169800-187172200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:187170000-187179800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:187170000-187180200	Weak transcription	Brain Angular Gyrus	brain
27	chr4:187170200-187175000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:187170200-187179200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:187170400-187172600	Enhancers	Liver	Liver
30	chr4:187170400-187173000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr4:187170400-187173200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:187170600-187171800	Enhancers	NHLF	lung
33	chr4:187170600-187172400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:187170600-187173000	Weak transcription	Brain Substantia Nigra	brain
35	chr4:187170800-187171400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr4:187170800-187171800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:187170800-187172200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:187170800-187174400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:187170800-187182000	Weak transcription	Right Ventricle	heart
40	chr4:187171000-187172200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr4:187171000-187172400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr4:187171000-187172600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:187171200-187171400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:187171200-187171400	Weak transcription	Gastric	stomach
45	chr4:187171200-187172000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
46	chr4:187171200-187172200	Enhancers	Fetal Stomach	stomach
47	chr4:187171200-187172400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr4:187171200-187182000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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