Variant report

Variant	rs4858564
Chromosome Location	chr3:23985852-23985853
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	FOXA1	chr3:23985621-23985947	HepG2	liver:	n/a	n/a
2	MYC	chr3:23985630-23988292	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23985779-23985795 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
3	CEBPB	chr3:23985542-23985860	K562	blood:	n/a	n/a
4	MYC	chr3:23985627-23988307	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23985779-23985795 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
5	CHD1	chr3:23985638-23986183	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:23985541-23990663	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr3:23985307-23988519	SK-N-SH	brain:	n/a	chr3:23987345-23987354
8	MAX	chr3:23985786-23986176	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:23985776-23985940	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:23985721-23986025	H1-hESC	embryonic stem cell:	n/a	n/a
11	USF1	chr3:23985666-23985977	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOXA2	chr3:23985618-23985856	HepG2	liver:	n/a	n/a
13	CEBPZ	chr3:23985719-23985901	HepG2	liver:	n/a	n/a
14	USF1	chr3:23985593-23986001	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOXA1	chr3:23985565-23985854	HepG2	liver:	n/a	n/a
16	FOXA1	chr3:23985608-23985856	HepG2	liver:	n/a	n/a
17	BHLHE40	chr3:23985728-23988393	K562	blood:	n/a	chr3:23986706-23986722 chr3:23986783-23986799 chr3:23987153-23987169 chr3:23987430-23987446 chr3:23987438-23987454 chr3:23987441-23987457 chr3:23987189-23987205
18	MXI1	chr3:23985536-23988397	IMR90	lung:	n/a	chr3:23987345-23987354
19	MAX	chr3:23985727-23985892	HepG2	liver:	n/a	chr3:23985779-23985795

No.	Distal block	Cell Line	Cell type
1	chr15:78422464..78425441-chr3:23985742..23987944,2	MCF-7	breast:
2	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
3	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
4	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region
ENSG00000166411	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000136425	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10084748	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs11129128	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129130	0.82[YRI][hapmap]
rs13070128	1.00[ASN][1000 genomes]
rs13087250	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316457	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	0.80[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321439	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321440	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1533141	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1567579	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058540	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34866549	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35755171	1.00[ASN][1000 genomes]
rs35755253	1.00[ASN][1000 genomes]
rs36063721	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935253	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66609380	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6775878	1.00[ASN][1000 genomes]
rs6776201	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6776568	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6778577	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6790140	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791805	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71324126	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72627094	0.82[AMR][1000 genomes]
rs73150266	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	1.00[ASN][1000 genomes]
rs7610935	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7611018	1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs954748	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs9812870	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9817923	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9853954	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855481	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs9863176	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882067	1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883834	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3449153	chr3:23984948-23988646	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3406325	chr3:23985473-23988321	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3425301	chr3:23985548-23988496	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23982200-23986000	Weak transcription	Right Atrium	heart
2	chr3:23985200-23986000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr3:23985200-23986000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:23985200-23986000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr3:23985200-23986000	Enhancers	Hela-S3	cervix
6	chr3:23985200-23986200	Flanking Active TSS	Fetal Heart	heart
7	chr3:23985200-23986200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:23985400-23986000	Enhancers	Placenta	Placenta
9	chr3:23985400-23986200	Enhancers	Primary B cells from peripheral blood	blood
10	chr3:23985400-23986600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr3:23985600-23986000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:23985600-23986000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:23985600-23986000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:23985600-23986000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:23985600-23986000	Enhancers	Brain Germinal Matrix	brain
16	chr3:23985600-23986000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr3:23985600-23986000	Bivalent Enhancer	Fetal Intestine Small	intestine
18	chr3:23985600-23986000	Bivalent/Poised TSS	NHEK	skin
19	chr3:23985600-23986200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
20	chr3:23985600-23986200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:23985600-23986200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr3:23985600-23986200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr3:23985600-23986200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr3:23985600-23986200	Flanking Active TSS	K562	blood
25	chr3:23985600-23986400	Bivalent/Poised TSS	Thymus	Thymus
26	chr3:23985600-23986600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:23985600-23988200	Active TSS	Fetal Kidney	kidney
28	chr3:23985600-23988400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:23985600-23988800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr3:23985800-23986000	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:23985800-23986000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:23985800-23986000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:23985800-23986000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr3:23985800-23986000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr3:23985800-23986000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr3:23985800-23986000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:23985800-23986000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:23985800-23986000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:23985800-23986000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
40	chr3:23985800-23986000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:23985800-23986000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:23985800-23986000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
43	chr3:23985800-23986000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:23985800-23986000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:23985800-23986000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:23985800-23986000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:23985800-23986000	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr3:23985800-23986000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
49	chr3:23985800-23986000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:23985800-23986000	Bivalent Enhancer	Fetal Intestine Large	intestine

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