Variant report

Variant	rs4479686
Chromosome Location	chr4:152399324-152399325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152393445..152396231-chr4:152399034..152401565,3	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10028035	0.83[EUR][1000 genomes]
rs10454251	0.86[EUR][1000 genomes]
rs10857260	0.86[EUR][1000 genomes]
rs11099815	0.83[EUR][1000 genomes]
rs11099816	0.86[EUR][1000 genomes]
rs11099819	0.86[EUR][1000 genomes]
rs11726254	0.84[EUR][1000 genomes]
rs11729923	0.87[EUR][1000 genomes]
rs11735957	0.86[EUR][1000 genomes]
rs11932398	0.88[EUR][1000 genomes]
rs12503602	0.86[CHB][hapmap]
rs12647555	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs1372976	0.85[EUR][1000 genomes]
rs1372977	0.84[EUR][1000 genomes]
rs1443087	0.85[EUR][1000 genomes]
rs1443088	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1443089	0.85[EUR][1000 genomes]
rs1443090	0.84[EUR][1000 genomes]
rs1470280	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1470281	0.86[EUR][1000 genomes]
rs1561918	0.85[EUR][1000 genomes]
rs1596290	0.88[EUR][1000 genomes]
rs1838043	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1899550	0.88[EUR][1000 genomes]
rs2034061	0.86[EUR][1000 genomes]
rs2053566	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2709812	0.80[EUR][1000 genomes]
rs2709813	0.83[EUR][1000 genomes]
rs2709814	0.81[EUR][1000 genomes]
rs2709815	0.83[EUR][1000 genomes]
rs2709816	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2709817	0.86[EUR][1000 genomes]
rs2709818	0.86[EUR][1000 genomes]
rs2709819	0.86[EUR][1000 genomes]
rs2709820	0.86[EUR][1000 genomes]
rs2709821	0.81[EUR][1000 genomes]
rs2709822	0.82[EUR][1000 genomes]
rs2709823	0.83[EUR][1000 genomes]
rs2709825	0.83[EUR][1000 genomes]
rs2709826	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2709827	0.80[EUR][1000 genomes]
rs2709828	0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2709829	0.83[EUR][1000 genomes]
rs2709831	0.84[EUR][1000 genomes]
rs2709832	0.84[EUR][1000 genomes]
rs2709833	0.84[EUR][1000 genomes]
rs2709834	0.83[EUR][1000 genomes]
rs2709838	0.83[EUR][1000 genomes]
rs2709842	0.83[EUR][1000 genomes]
rs2709844	0.83[EUR][1000 genomes]
rs2724547	0.83[EUR][1000 genomes]
rs2724550	0.83[EUR][1000 genomes]
rs2724551	0.83[EUR][1000 genomes]
rs2724553	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2724555	0.83[EUR][1000 genomes]
rs2724556	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2724563	0.83[EUR][1000 genomes]
rs2724564	0.83[EUR][1000 genomes]
rs2724567	0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2724568	0.83[EUR][1000 genomes]
rs2724571	0.83[EUR][1000 genomes]
rs2724574	0.86[EUR][1000 genomes]
rs2724577	0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2724578	0.83[EUR][1000 genomes]
rs2724580	0.83[EUR][1000 genomes]
rs28549769	0.88[EUR][1000 genomes]
rs28622593	0.83[EUR][1000 genomes]
rs28666858	0.86[EUR][1000 genomes]
rs3929153	0.85[EUR][1000 genomes]
rs4235219	0.82[EUR][1000 genomes]
rs4263379	0.88[EUR][1000 genomes]
rs4266275	0.83[EUR][1000 genomes]
rs4355371	0.85[EUR][1000 genomes]
rs4696088	0.83[EUR][1000 genomes]
rs4696089	0.87[EUR][1000 genomes]
rs4696092	0.88[EUR][1000 genomes]
rs56301462	0.84[EUR][1000 genomes]
rs6825069	0.85[EUR][1000 genomes]
rs6843639	0.88[EUR][1000 genomes]
rs6845344	0.85[EUR][1000 genomes]
rs6845648	0.83[EUR][1000 genomes]
rs6851814	0.82[EUR][1000 genomes]
rs6855845	0.85[EUR][1000 genomes]
rs7657670	0.83[EUR][1000 genomes]
rs7657747	0.87[EUR][1000 genomes]
rs7658169	0.83[EUR][1000 genomes]
rs7666571	0.85[EUR][1000 genomes]
rs7676059	0.87[EUR][1000 genomes]
rs7676493	0.86[EUR][1000 genomes]
rs7676922	0.83[EUR][1000 genomes]
rs7677131	0.83[EUR][1000 genomes]
rs7678823	0.83[EUR][1000 genomes]
rs7680013	0.88[EUR][1000 genomes]
rs7680236	0.88[EUR][1000 genomes]
rs7682770	0.87[EUR][1000 genomes]
rs7682837	0.86[EUR][1000 genomes]
rs7684462	0.83[EUR][1000 genomes]
rs7698816	0.83[EUR][1000 genomes]
rs9994482	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv432643	chr4:152335395-152417635	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4479686	FAM160A1	cis	parietal	SCAN
rs4479686	FAM160A1	cis	Whole Blood	GTEx
rs4479686	PET112L	cis	multi-tissue	Pritchard
rs4479686	PET112L	cis	parietal	SCAN
rs4479686	PET112L	cis	lymphoblastoid	seeQTL
rs4479686	FAM160A1	cis	cerebellum	SCAN
rs4479686	SH3D19	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152391800-152405400	Weak transcription	NHEK	skin
2	chr4:152395000-152413200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr4:152396000-152400800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:152396000-152400800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:152396600-152399800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:152396800-152400200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:152396800-152400600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:152396800-152400800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:152396800-152401200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:152396800-152404600	Weak transcription	HSMM	muscle
11	chr4:152396800-152405400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:152396800-152405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:152397000-152400600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:152397000-152401400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:152397200-152406600	Weak transcription	Psoas Muscle	Psoas
16	chr4:152399200-152399400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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