Variant report

Variant	rs4518223
Chromosome Location	chr4:175340298-175340299
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	FOS	chr4:175340004-175340404	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF7L2	chr4:175339718-175340377	Hela-S3	cervix:	n/a	n/a
3	FOS	chr4:175340043-175340403	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr4:175339755-175340392	Hela-S3	cervix:	n/a	chr4:175339962-175339975 chr4:175339963-175339974 chr4:175339962-175339975 chr4:175339962-175339975
5	STAT3	chr4:175340184-175340323	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr4:175339818-175340347	MCF10A-Er-Src	breast:	n/a	chr4:175339908-175339917
7	PRDM1	chr4:175339886-175340330	Hela-S3	cervix:	n/a	n/a
8	FOS	chr4:175340147-175340343	MCF10A-Er-Src	breast:	n/a	n/a
9	RFX5	chr4:175339897-175340315	Hela-S3	cervix:	n/a	n/a
10	STAT3	chr4:175339855-175340317	Hela-S3	cervix:	n/a	n/a
11	EP300	chr4:175339784-175340360	Hela-S3	cervix:	n/a	chr4:175340173-175340183 chr4:175340010-175340018 chr4:175340317-175340331 chr4:175340319-175340333 chr4:175339960-175339974
12	STAT3	chr4:175340032-175340379	MCF10A-Er-Src	breast:	n/a	chr4:175340317-175340328
13	BRCA1	chr4:175339813-175340324	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr4:175339738-175340362	Hela-S3	cervix:	n/a	n/a
15	NR2F2	chr4:175339982-175340339	MCF-7	breast:	n/a	chr4:175340208-175340223
16	CHD2	chr4:175340001-175340383	Hela-S3	cervix:	n/a	n/a
17	MYC	chr4:175340175-175340303	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MIR4276	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11725800	0.82[ASN][1000 genomes]
rs11727574	0.81[ASN][1000 genomes]
rs11732436	0.81[EUR][1000 genomes]
rs11732586	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11735455	0.81[ASN][1000 genomes]
rs13101376	0.81[ASN][1000 genomes]
rs13102962	0.81[ASN][1000 genomes]
rs13107351	0.82[ASN][1000 genomes]
rs13108930	0.82[ASN][1000 genomes]
rs13109756	0.81[ASN][1000 genomes]
rs13112972	0.87[ASN][1000 genomes]
rs13119359	0.88[ASN][1000 genomes]
rs13120534	0.81[ASN][1000 genomes]
rs13122946	0.82[ASN][1000 genomes]
rs13132617	0.82[ASN][1000 genomes]
rs13135662	0.88[ASN][1000 genomes]
rs13140627	0.82[ASN][1000 genomes]
rs13146439	0.82[ASN][1000 genomes]
rs13149585	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149810	0.82[ASN][1000 genomes]
rs13150656	0.82[ASN][1000 genomes]
rs13152348	0.89[ASN][1000 genomes]
rs1922383	0.81[ASN][1000 genomes]
rs28519075	0.81[ASN][1000 genomes]
rs34037587	0.82[ASN][1000 genomes]
rs34054930	0.86[ASN][1000 genomes]
rs34135350	0.86[ASN][1000 genomes]
rs34175211	0.85[ASN][1000 genomes]
rs34572193	0.82[ASN][1000 genomes]
rs34592304	0.86[ASN][1000 genomes]
rs34604934	0.82[ASN][1000 genomes]
rs34674779	0.89[ASN][1000 genomes]
rs34795808	0.81[ASN][1000 genomes]
rs34833822	0.82[ASN][1000 genomes]
rs35078417	0.81[ASN][1000 genomes]
rs35211627	0.86[ASN][1000 genomes]
rs35263478	0.82[ASN][1000 genomes]
rs35295528	0.82[ASN][1000 genomes]
rs35326753	0.84[ASN][1000 genomes]
rs35347093	0.81[ASN][1000 genomes]
rs35423027	0.85[ASN][1000 genomes]
rs35539859	0.80[ASN][1000 genomes]
rs35663303	0.82[ASN][1000 genomes]
rs35706347	0.89[ASN][1000 genomes]
rs35760448	0.81[ASN][1000 genomes]
rs35794791	0.84[ASN][1000 genomes]
rs35920928	0.80[ASN][1000 genomes]
rs35931018	0.93[ASN][1000 genomes]
rs35978128	0.82[ASN][1000 genomes]
rs36122870	0.82[ASN][1000 genomes]
rs3980460	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4273447	0.81[ASN][1000 genomes]
rs4518224	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4568217	0.81[ASN][1000 genomes]
rs4695929	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62337061	0.81[ASN][1000 genomes]
rs62337062	0.81[ASN][1000 genomes]
rs62337063	0.81[ASN][1000 genomes]
rs62337086	0.82[ASN][1000 genomes]
rs62337087	0.82[ASN][1000 genomes]
rs6553785	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6553786	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6553789	0.81[ASN][1000 genomes]
rs6553790	0.81[ASN][1000 genomes]
rs6553791	0.81[ASN][1000 genomes]
rs67728476	0.81[ASN][1000 genomes]
rs6812366	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6827853	0.82[ASN][1000 genomes]
rs6852435	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs6853004	0.81[ASN][1000 genomes]
rs6853166	0.81[ASN][1000 genomes]
rs6853181	0.81[ASN][1000 genomes]
rs7654427	0.81[ASN][1000 genomes]
rs7655606	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7665426	0.82[ASN][1000 genomes]
rs7665708	0.81[ASN][1000 genomes]
rs7667325	0.81[ASN][1000 genomes]
rs7667374	0.81[ASN][1000 genomes]
rs7667642	0.81[ASN][1000 genomes]
rs7672838	0.81[ASN][1000 genomes]
rs7677994	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7680564	0.81[ASN][1000 genomes]
rs7687802	0.81[ASN][1000 genomes]
rs7688229	0.81[ASN][1000 genomes]
rs7689422	0.81[ASN][1000 genomes]
rs7691061	0.81[ASN][1000 genomes]
rs7693269	0.89[ASN][1000 genomes]
rs7695912	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4518223	VEGFC	cis	parietal	SCAN
rs4518223	FBXO8	cis	parietal	SCAN
rs4518223	KIAA1712	cis	parietal	SCAN
rs4518223	NXF1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175336800-175340600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:175339800-175340600	Enhancers	Hela-S3	cervix
3	chr4:175340000-175340800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:175340200-175344200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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