Variant report

Variant	rs1560167
Chromosome Location	chr5:54170865-54170866
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	CEBPB	chr5:54170301-54170907	MCF-7	breast:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
2	NFIC	chr5:54170024-54170870	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr5:54170149-54170891	T-47D	breast:	n/a	n/a
4	ZKSCAN1	chr5:54170389-54171119	Hela-S3	cervix:	n/a	n/a
5	SPI1	chr5:54170414-54170970	HL-60	blood:	n/a	n/a
6	GATA3	chr5:54170103-54170883	MCF-7	breast:	n/a	n/a
7	GATA3	chr5:54170214-54170870	T-47D	breast:	n/a	n/a
8	CEBPB	chr5:54170325-54170939	MCF-7	breast:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651

Variant related genes	Relation type
ENSG00000249843	TF binding region
ENSG00000232517	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10040872	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10042734	0.91[ASN][1000 genomes]
rs1005622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10056452	0.97[ASN][1000 genomes]
rs10940430	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940431	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10940432	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10940434	0.96[ASN][1000 genomes]
rs11738151	0.96[ASN][1000 genomes]
rs11742711	0.96[ASN][1000 genomes]
rs11953607	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12657845	0.96[ASN][1000 genomes]
rs13181749	0.98[ASN][1000 genomes]
rs1560165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1560166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17588816	0.83[ASN][1000 genomes]
rs1988528	0.81[EUR][1000 genomes]
rs1991498	0.87[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2017082	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2017318	0.81[EUR][1000 genomes]
rs2017540	0.81[EUR][1000 genomes]
rs2019005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2195392	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2195393	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2407758	0.81[EUR][1000 genomes]
rs28564901	0.84[ASN][1000 genomes]
rs3916738	0.91[ASN][1000 genomes]
rs4242050	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4320216	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4502767	0.93[ASN][1000 genomes]
rs4865586	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs4865879	0.98[ASN][1000 genomes]
rs4865880	0.98[ASN][1000 genomes]
rs4865881	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865882	0.96[ASN][1000 genomes]
rs4865883	0.81[EUR][1000 genomes]
rs6860824	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs737526	0.89[ASN][1000 genomes]
rs7709516	0.85[ASN][1000 genomes]
rs981978	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54168400-54171800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:54168600-54175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:54169000-54171000	Enhancers	HUVEC	blood vessel
4	chr5:54169400-54171000	Enhancers	Osteobl	bone
5	chr5:54169400-54171400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:54169400-54171800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:54169600-54171000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:54169600-54171000	Enhancers	Adipose Nuclei	Adipose
9	chr5:54169600-54171400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:54169600-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:54169600-54171400	Enhancers	Hela-S3	cervix
12	chr5:54169800-54171000	Enhancers	Liver	Liver
13	chr5:54169800-54171200	Weak transcription	Left Ventricle	heart
14	chr5:54170000-54171200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr5:54170000-54171400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:54170200-54171000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:54170200-54171200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:54170200-54171200	Enhancers	Fetal Lung	lung
22	chr5:54170200-54171400	Enhancers	Primary hematopoietic stem cells	blood
23	chr5:54170200-54171400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:54170200-54171400	Enhancers	Stomach Mucosa	stomach
25	chr5:54170200-54172400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:54170200-54172400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:54170600-54171200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:54170600-54172400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:54170600-54172600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:54170800-54171400	Enhancers	H9 Cell Line	embryonic stem cell
31	chr5:54170800-54171400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:54170800-54171400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
33	chr5:54170800-54172400	Weak transcription	Fetal Intestine Small	intestine
34	chr5:54170800-54175800	Weak transcription	NHEK	skin

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