Variant report

Variant	rs13104485
Chromosome Location	chr4:100140823-100140824
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	FOXA2	chr4:100139918-100141135	HepG2	liver:	n/a	n/a
2	EP300	chr4:100140166-100141001	HepG2	liver:	n/a	chr4:100140839-100140853 chr4:100140259-100140266
3	SPI1	chr4:100140679-100140977	GM12891	blood:	n/a	chr4:100140841-100140848 chr4:100140844-100140853
4	SPI1	chr4:100140679-100141010	GM12891	blood:	n/a	chr4:100140841-100140848 chr4:100140844-100140853
5	POU2F2	chr4:100140746-100140978	GM12891	blood:	n/a	chr4:100140853-100140866 chr4:100140854-100140868 chr4:100140857-100140865 chr4:100140854-100140866 chr4:100140856-100140867 chr4:100140856-100140867 chr4:100140857-100140864 chr4:100140856-100140865 chr4:100140856-100140866 chr4:100140853-100140868 chr4:100140855-100140865 chr4:100140852-100140870 chr4:100140855-100140865
6	FOXA2	chr4:100140651-100140894	HepG2	liver:	n/a	n/a
7	POU2F2	chr4:100140698-100140938	GM12878	blood:	n/a	chr4:100140853-100140866 chr4:100140854-100140868 chr4:100140857-100140865 chr4:100140854-100140866 chr4:100140856-100140867 chr4:100140856-100140867 chr4:100140857-100140864 chr4:100140856-100140865 chr4:100140856-100140866 chr4:100140853-100140868 chr4:100140855-100140865 chr4:100140852-100140870 chr4:100140855-100140865
8	SPI1	chr4:100140479-100141246	GM12878	blood:	n/a	chr4:100140841-100140848 chr4:100140844-100140853
9	FOXA1	chr4:100140098-100140988	HepG2	liver:	n/a	n/a
10	SPI1	chr4:100140707-100141029	GM12878	blood:	n/a	chr4:100140841-100140848 chr4:100140844-100140853
11	NFIC	chr4:100139954-100140876	HepG2	liver:	n/a	n/a
12	MYBL2	chr4:100140008-100140851	HepG2	liver:	n/a	n/a
13	SPI1	chr4:100140731-100140880	GM12878	blood:	n/a	chr4:100140841-100140848 chr4:100140844-100140853
14	TCF7L2	chr4:100139917-100140860	HepG2	liver:	n/a	chr4:100140100-100140114
15	ARID3A	chr4:100140191-100140988	HepG2	liver:	n/a	n/a
16	TEAD4	chr4:100139996-100140964	HepG2	liver:	n/a	n/a
17	POU2F2	chr4:100140745-100141016	GM12891	blood:	n/a	chr4:100140853-100140866 chr4:100140854-100140868 chr4:100140857-100140865 chr4:100140854-100140866 chr4:100140856-100140867 chr4:100140856-100140867 chr4:100140857-100140864 chr4:100140856-100140865 chr4:100140856-100140866 chr4:100140853-100140868 chr4:100140855-100140865 chr4:100140852-100140870 chr4:100140855-100140865
18	FOXA1	chr4:100140039-100140933	HepG2	liver:	n/a	n/a
19	REST	chr4:100140709-100140911	Hela-S3	cervix:	n/a	n/a
20	FOXA1	chr4:100140248-100141002	HepG2	liver:	n/a	n/a
21	POU2F2	chr4:100140735-100141090	GM12878	blood:	n/a	chr4:100140853-100140866 chr4:100140854-100140868 chr4:100140857-100140865 chr4:100140854-100140866 chr4:100140856-100140867 chr4:100140856-100140867 chr4:100140857-100140864 chr4:100140856-100140865 chr4:100140856-100140866 chr4:100140853-100140868 chr4:100140855-100140865 chr4:100140852-100140870 chr4:100140855-100140865

Variant related genes	Relation type
ADH6	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12498658	0.81[ASN][1000 genomes]
rs12501204	0.84[ASN][1000 genomes]
rs12506882	0.84[ASN][1000 genomes]
rs12507078	0.92[CHB][hapmap]
rs12507573	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12512084	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13117371	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1497378	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17584051	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2010612	0.81[ASN][1000 genomes]
rs2173199	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2201728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866151	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28914783	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28914793	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3749550	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3749551	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4147531	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4147532	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4269183	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4699381	0.84[ASN][1000 genomes]
rs4699734	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs57428460	0.84[ASN][1000 genomes]
rs58660705	0.84[ASN][1000 genomes]
rs58827689	0.84[ASN][1000 genomes]
rs60345995	0.84[ASN][1000 genomes]
rs6532814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72679847	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72679867	0.84[ASN][1000 genomes]
rs72679874	0.84[ASN][1000 genomes]
rs7654607	0.84[ASN][1000 genomes]
rs7663369	0.84[ASN][1000 genomes]
rs7669335	0.84[ASN][1000 genomes]
rs7678074	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692358	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100108400-100141600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:100127000-100142600	Weak transcription	Small Intestine	intestine
3	chr4:100129000-100143200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:100131400-100143000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:100139400-100141000	Enhancers	Fetal Intestine Small	intestine
6	chr4:100139800-100141000	Enhancers	Fetal Intestine Large	intestine
7	chr4:100139800-100141000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr4:100140000-100141000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:100140200-100141000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr4:100140200-100141000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:100140200-100141000	Enhancers	Pancreas	Pancrea
12	chr4:100140200-100141000	Enhancers	Stomach Mucosa	stomach
13	chr4:100140200-100141200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:100140200-100141200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr4:100140200-100141400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr4:100140400-100141000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr4:100140400-100142600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:100140400-100143000	Weak transcription	Fetal Kidney	kidney
19	chr4:100140600-100141000	Enhancers	Fetal Lung	lung
20	chr4:100140600-100141000	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr4:100140600-100141200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr4:100140600-100143600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:100140800-100141200	Flanking Active TSS	HepG2	liver
24	chr4:100140800-100141600	Enhancers	Liver	Liver

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