Variant report

Variant	rs1870013
Chromosome Location	chr5:59997412-59997413
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	BHLHE40	chr5:59995469-59997496	K562	blood:	n/a	chr5:59995940-59995956 chr5:59995931-59995947
2	POLR2A	chr5:59995082-59997876	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr5:59997360-59997660	K562	blood:	n/a	n/a
4	TEAD4	chr5:59997366-59997881	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr5:59995354-59997661	K562	blood:	n/a	n/a
6	GATA1	chr5:59995405-59997530	PBDE	blood:	n/a	n/a
7	POLR2A	chr5:59994810-59998074	K562	blood:	n/a	n/a
8	JUND	chr5:59997102-59997641	K562	blood:	n/a	n/a
9	CEBPB	chr5:59997356-59997558	K562	blood:	n/a	n/a
10	NR2F2	chr5:59997147-59997522	K562	blood:	n/a	n/a
11	POLR2A	chr5:59997279-59997594	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:59994474..59997876-chr5:60455928..60460228,5	K562	blood:
2	chr5:59995106..59997535-chr5:60240120..60242292,3	K562	blood:
3	chr5:59995886..59998322-chr5:60239584..60242446,2	MCF-7	breast:
4	chr5:59996423..59998684-chr5:60001090..60003995,3	MCF-7	breast:

Variant related genes	Relation type
DEPDC1B	TF binding region
ENSG00000164182	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000049167	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1026418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1107233	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12658660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379113	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460959	0.93[CHB][hapmap]
rs1563516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1563517	0.93[CHB][hapmap]
rs1563518	0.91[CHB][hapmap]
rs1563519	0.93[CHB][hapmap]
rs1563905	0.93[CHB][hapmap]
rs1563906	0.91[CHB][hapmap]
rs1563907	0.93[CHB][hapmap]
rs16878304	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs16878315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1870012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992613	0.93[CHB][hapmap]
rs2045355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061254	1.00[CEU][hapmap]
rs2124751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124753	0.83[ASN][1000 genomes]
rs2169254	0.93[CHB][hapmap]
rs2305680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2591635	1.00[CEU][hapmap]
rs2606688	1.00[CEU][hapmap]
rs286150	1.00[CEU][hapmap]
rs286152	1.00[CEU][hapmap]
rs286157	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2898298	0.93[CHB][hapmap]
rs34414908	0.83[ASN][1000 genomes]
rs34915115	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857238	0.93[CHB][hapmap]
rs4273559	0.93[CHB][hapmap]
rs61752571	0.85[ASN][1000 genomes]
rs6871928	0.93[CHB][hapmap]
rs6872509	1.00[CEU][hapmap]
rs7702459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7713673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7716051	0.93[CHB][hapmap]
rs7719525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs881066	0.82[ASN][1000 genomes]
rs897671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv1794154	chr5:59995393-60012235	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1821070	chr5:59995393-60012235	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv1801919	chr5:59995393-60013913	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59996600-59997600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr5:59996600-59997600	Enhancers	Left Ventricle	heart
3	chr5:59996600-59997600	Enhancers	Small Intestine	intestine
4	chr5:59996600-59997800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:59996600-59998200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:59996800-59997600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr5:59996800-59997600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:59996800-59997600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:59996800-59997600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:59996800-59997600	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr5:59996800-59997800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:59996800-59997800	Enhancers	Fetal Intestine Large	intestine
13	chr5:59996800-59998000	Enhancers	Fetal Intestine Small	intestine
14	chr5:59996800-60001800	Enhancers	Placenta	Placenta
15	chr5:59997000-59997600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:59997000-59997600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:59997000-59997600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:59997000-59997600	Enhancers	Adipose Nuclei	Adipose
19	chr5:59997000-59997600	Enhancers	Fetal Lung	lung
20	chr5:59997000-59997600	Enhancers	A549	lung
21	chr5:59997000-59997600	Enhancers	HepG2	liver
22	chr5:59997000-59997600	Enhancers	NHEK	skin
23	chr5:59997000-59997800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:59997000-59998000	Enhancers	HMEC	breast
25	chr5:59997000-59998000	Enhancers	K562	blood
26	chr5:59997000-59999600	Weak transcription	Stomach Mucosa	stomach
27	chr5:59997200-59997600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:59997400-59997600	Enhancers	Monocytes-CD14+_RO01746	blood

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