Variant report

Variant	rs73173912
Chromosome Location	chr3:19989960-19989961
allele	A/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	CUX1	chr3:19989021-19990564	K562	blood:	n/a	n/a
2	TBP	chr3:19986938-19989974	K562	blood:	n/a	n/a
3	MAFK	chr3:19989728-19990036	HepG2	liver:	n/a	chr3:19989882-19989896 chr3:19989881-19989897 chr3:19989884-19989899 chr3:19989888-19989899 chr3:19989879-19989899
4	MAFK	chr3:19988897-19990057	Hela-S3	cervix:	n/a	chr3:19989882-19989896 chr3:19989888-19989899 chr3:19989881-19989897 chr3:19989884-19989899 chr3:19989879-19989899
5	POLR2A	chr3:19986589-19991063	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA1	chr3:19987428-19990353	PBDE	blood:	n/a	chr3:19990147-19990157
7	TAL1	chr3:19986884-19990195	K562	blood:	n/a	chr3:19989618-19989626
8	CHD1	chr3:19987459-19990325	IMR90	lung:	n/a	chr3:19989363-19989373
9	CHD1	chr3:19989651-19990103	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr3:19987947-19990015	IMR90	lung:	n/a	n/a
11	MAFF	chr3:19989714-19990026	HepG2	liver:	n/a	chr3:19989882-19989896 chr3:19989883-19989901
12	KAP1	chr3:19989253-19990000	K562	blood:	n/a	n/a
13	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a
14	EP300	chr3:19986934-19990338	K562	blood:	n/a	chr3:19989189-19989198 chr3:19987240-19987247 chr3:19988330-19988346 chr3:19989873-19989887 chr3:19990149-19990158 chr3:19988621-19988637 chr3:19990026-19990040
15	IRF1	chr3:19986750-19990360	K562	blood:	n/a	chr3:19990060-19990067 chr3:19987995-19988009 chr3:19988390-19988404
16	MAFK	chr3:19989781-19990065	HepG2	liver:	n/a	chr3:19989882-19989896 chr3:19989888-19989899 chr3:19989881-19989897 chr3:19989884-19989899 chr3:19989879-19989899
17	TRIM28	chr3:19987159-19990037	K562	blood:	n/a	chr3:19989187-19989196 chr3:19989190-19989199
18	IRF1	chr3:19986493-19990740	K562	blood:	n/a	chr3:19990060-19990067 chr3:19987995-19988009 chr3:19988390-19988404
19	MYC	chr3:19986767-19990058	K562	blood:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
20	POLR2A	chr3:19987841-19990881	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987782..19990680-chr3:20013275..20017779,4	K562	blood:
3	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
4	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
5	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
6	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
7	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:
8	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

Variant related genes	Relation type
RAB5A	TF binding region
EFHB	TF binding region
ENSG00000129810	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11924875	1.00[EUR][1000 genomes]
rs11925668	1.00[AMR][1000 genomes]
rs11929340	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13317268	1.00[AMR][1000 genomes]
rs13340108	1.00[EUR][1000 genomes]
rs1605195	1.00[EUR][1000 genomes]
rs17006349	1.00[EUR][1000 genomes]
rs2001650	1.00[EUR][1000 genomes]
rs28886381	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55746682	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55851373	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58512353	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58603530	1.00[EUR][1000 genomes]
rs59572420	0.81[AFR][1000 genomes]
rs61068672	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61139478	1.00[EUR][1000 genomes]
rs61152961	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6550130	1.00[EUR][1000 genomes]
rs6550210	1.00[EUR][1000 genomes]
rs6550212	1.00[EUR][1000 genomes]
rs6550216	1.00[EUR][1000 genomes]
rs6791245	1.00[EUR][1000 genomes]
rs6805780	1.00[EUR][1000 genomes]
rs73176006	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73176093	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73184830	1.00[EUR][1000 genomes]
rs73184831	1.00[EUR][1000 genomes]
rs73184832	1.00[EUR][1000 genomes]
rs73184839	1.00[EUR][1000 genomes]
rs73184842	1.00[EUR][1000 genomes]
rs73188422	1.00[AMR][1000 genomes]
rs73190456	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73190462	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355793	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624970	1.00[EUR][1000 genomes]
rs7629079	1.00[EUR][1000 genomes]
rs7651609	1.00[EUR][1000 genomes]
rs9834480	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840739	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9847647	1.00[EUR][1000 genomes]
rs9850421	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9850795	1.00[AMR][1000 genomes]
rs9854666	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855399	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861798	1.00[EUR][1000 genomes]
rs9869783	1.00[AMR][1000 genomes]
rs9875453	1.00[AMR][1000 genomes]
rs9881822	1.00[EUR][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	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19986800-19990200	Active TSS	Duodenum Mucosa	Duodenum
2	chr3:19987200-19990400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:19987200-19990400	Active TSS	Placenta	Placenta
4	chr3:19987200-19990600	Active TSS	K562	blood
5	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:19987400-19990000	Active TSS	Brain Germinal Matrix	brain
7	chr3:19987400-19990000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr3:19987400-19990000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:19987400-19990000	Active TSS	A549	lung
10	chr3:19987400-19990200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:19987400-19990200	Active TSS	HSMM	muscle
12	chr3:19987400-19990400	Active TSS	NHDF-Ad	bronchial
13	chr3:19987400-19990800	Active TSS	Right Atrium	heart
14	chr3:19987400-19990800	Active TSS	HSMMtube	muscle
15	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:19987600-19990000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:19987600-19990000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:19987600-19990000	Active TSS	Ovary	ovary
19	chr3:19987600-19990000	Active TSS	Thymus	Thymus
20	chr3:19987600-19990200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:19987600-19990200	Active TSS	Colon Smooth Muscle	Colon
22	chr3:19987600-19990400	Active TSS	Colonic Mucosa	Colon
23	chr3:19987600-19990400	Active TSS	Fetal Kidney	kidney
24	chr3:19987600-19990800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr3:19987600-19991000	Active TSS	NHLF	lung
26	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:19987800-19990000	Active TSS	Aorta	Aorta
28	chr3:19987800-19990000	Active TSS	Fetal Muscle Trunk	muscle
29	chr3:19987800-19990000	Active TSS	Stomach Mucosa	stomach
30	chr3:19987800-19990400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr3:19987800-19990400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:19987800-19990800	Active TSS	Psoas Muscle	Psoas
33	chr3:19987800-19990800	Active TSS	Right Ventricle	heart
34	chr3:19987800-19991400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr3:19987800-19991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:19988000-19990000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:19988000-19990000	Active TSS	Fetal Intestine Small	intestine
38	chr3:19988000-19990000	Active TSS	Fetal Lung	lung
39	chr3:19988000-19990000	Active TSS	Placenta Amnion	Placenta Amnion
40	chr3:19988000-19990200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr3:19988000-19990200	Active TSS	GM12878-XiMat	blood
42	chr3:19988000-19990400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:19988000-19990400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr3:19988000-19990400	Active TSS	NHEK	skin
45	chr3:19988000-19990600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:19988000-19990600	Active TSS	Stomach Smooth Muscle	stomach
47	chr3:19988000-19990600	Active TSS	HMEC	breast
48	chr3:19988000-19990800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:19988000-19991200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr3:19988000-19991400	Active TSS	iPS-15b Cell Line	embryonic stem cell

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