Variant report

Variant	rs17181337
Chromosome Location	chr3:19990535-19990536
allele	A/G
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	POLR2A	chr3:19986589-19991063	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a
4	STAT3	chr3:19990421-19990697	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:19990061-19991082	GM12878	blood:	n/a	n/a
6	IRF1	chr3:19986493-19990740	K562	blood:	n/a	chr3:19990060-19990067 chr3:19987995-19988009 chr3:19988390-19988404
7	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	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:
6	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

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

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10510497	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374092	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486167	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486526	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488378	1.00[ASN][1000 genomes]
rs12490848	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495866	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497549	1.00[ASN][1000 genomes]
rs17796230	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365374	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28597881	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866630	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241539	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398451	1.00[ASN][1000 genomes]
rs45542931	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618239	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858116	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858632	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858662	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858674	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797296	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892327	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029370	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241280	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241285	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241286	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62241289	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241295	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241316	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241322	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241326	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241330	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241333	1.00[ASN][1000 genomes]
rs62241334	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241337	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62243065	1.00[ASN][1000 genomes]
rs62243074	1.00[ASN][1000 genomes]
rs62243075	1.00[ASN][1000 genomes]
rs62243076	1.00[ASN][1000 genomes]
rs73032477	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034166	1.00[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	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19987200-19990600	Active TSS	K562	blood
2	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:19987400-19990800	Active TSS	Right Atrium	heart
4	chr3:19987400-19990800	Active TSS	HSMMtube	muscle
5	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:19987600-19990800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:19987600-19991000	Active TSS	NHLF	lung
8	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:19987800-19990800	Active TSS	Psoas Muscle	Psoas
10	chr3:19987800-19990800	Active TSS	Right Ventricle	heart
11	chr3:19987800-19991400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr3:19987800-19991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:19988000-19990600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:19988000-19990600	Active TSS	Stomach Smooth Muscle	stomach
15	chr3:19988000-19990600	Active TSS	HMEC	breast
16	chr3:19988000-19990800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:19988000-19991200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:19988000-19991400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:19988200-19990600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr3:19988200-19990800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:19988200-19990800	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:19988200-19990800	Active TSS	Fetal Muscle Leg	muscle
23	chr3:19988200-19991600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:19988200-19991600	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr3:19989000-19990800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr3:19989400-19990600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:19989400-19990600	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr3:19989400-19990600	Active TSS	HepG2	liver
29	chr3:19989400-19990800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:19989400-19991000	Flanking Active TSS	Fetal Brain Female	brain
31	chr3:19989400-19991400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:19989600-19990600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr3:19989600-19990600	Flanking Active TSS	Liver	Liver
34	chr3:19989600-19990600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr3:19989600-19991000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr3:19989600-19991000	Flanking Active TSS	Dnd41	blood
37	chr3:19989600-19991200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:19989600-19991400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:19989800-19990800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:19989800-19990800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:19989800-19990800	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr3:19989800-19990800	Weak transcription	Left Ventricle	heart
43	chr3:19989800-19990800	Weak transcription	Pancreas	Pancrea
44	chr3:19989800-19990800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:19989800-19991200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr3:19989800-19991200	Weak transcription	Lung	lung
47	chr3:19989800-19991800	Weak transcription	Small Intestine	intestine
48	chr3:19989800-19993000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:19989800-19993000	Weak transcription	Esophagus	oesophagus
50	chr3:19989800-19993000	Weak transcription	Spleen	Spleen

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