Variant report

Variant	rs56040704
Chromosome Location	chr16:72127792-72127793
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	SIN3AK20	chr16:72127267-72128056	A549	lung:	n/a	n/a
2	NFYB	chr16:72127423-72128033	GM12878	blood:	n/a	chr16:72127664-72127674 chr16:72127663-72127678 chr16:72127663-72127676
3	CUX1	chr16:72127545-72127833	K562	blood:	n/a	n/a
4	POLR2A	chr16:72127171-72128405	Hela-S3	cervix:	n/a	n/a
5	GATA1	chr16:72127390-72128506	PBDE	blood:	n/a	chr16:72127614-72127624
6	ETS1	chr16:72127276-72128046	GM12878	blood:	n/a	chr16:72127558-72127567 chr16:72127516-72127523 chr16:72127558-72127567
7	CREB1	chr16:72127239-72128278	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:72127273-72127966	HCT-116	colon:	n/a	n/a
9	POLR2A	chr16:72127250-72128400	U87	brain:	n/a	n/a
10	EGR1	chr16:72127270-72128023	H1-hESC	embryonic stem cell:	n/a	chr16:72127535-72127542 chr16:72127896-72127905
11	MAX	chr16:72127251-72128091	HepG2	liver:	n/a	chr16:72127351-72127360
12	MYBL2	chr16:72126783-72128085	HepG2	liver:	n/a	n/a
13	ELK1	chr16:72127335-72127949	Hela-S3	cervix:	n/a	chr16:72127558-72127567 chr16:72127558-72127567
14	SIX5	chr16:72127451-72128119	GM12878	blood:	n/a	n/a
15	USF2	chr16:72127442-72127850	Hela-S3	cervix:	n/a	n/a
16	EP300	chr16:72127294-72127997	GM12878	blood:	n/a	chr16:72127492-72127501
17	POLR2A	chr16:72127187-72128367	GM19193	blood:	n/a	n/a
18	ATF3	chr16:72127419-72127803	K562	blood:	n/a	n/a
19	MYC	chr16:72127645-72127889	HUVEC	blood vessel:	n/a	n/a
20	SIN3A	chr16:72126770-72128640	H1-hESC	embryonic stem cell:	n/a	chr16:72127343-72127351 chr16:72127337-72127350
21	GTF2F1	chr16:72127372-72128139	K562	blood:	n/a	n/a
22	TCF12	chr16:72127650-72127972	GM12878	blood:	n/a	n/a
23	POLR2A	chr16:72126738-72128525	Hela-S3	cervix:	n/a	n/a
24	ETS1	chr16:72127283-72127993	A549	lung:	n/a	chr16:72127558-72127567 chr16:72127516-72127523 chr16:72127558-72127567
25	TAF1	chr16:72126780-72128439	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD2	chr16:72126842-72128038	Hela-S3	cervix:	n/a	n/a
27	BRCA1	chr16:72127623-72127912	GM12878	blood:	n/a	n/a
28	NFIC	chr16:72127166-72128084	HepG2	liver:	n/a	n/a
29	POLR2A	chr16:72127138-72128133	HL-60	blood:	n/a	n/a
30	GABPA	chr16:72126579-72128509	A549	lung:	n/a	chr16:72127456-72127470
31	REST	chr16:72127119-72128199	HL-60	blood:	n/a	chr16:72127341-72127350 chr16:72127337-72127350 chr16:72127344-72127352
32	SMC3	chr16:72127517-72127874	HepG2	liver:	n/a	n/a
33	MXI1	chr16:72126947-72128235	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr16:72127291-72127935	Hela-S3	cervix:	n/a	n/a
35	MAX	chr16:72126970-72128038	SK-N-SH	brain:	n/a	chr16:72127351-72127360
36	EBF1	chr16:72127285-72127895	GM12878	blood:	n/a	n/a
37	MAX	chr16:72127118-72128089	MCF-7	breast:	n/a	chr16:72127351-72127360
38	TBP	chr16:72127189-72128216	H1-hESC	embryonic stem cell:	n/a	n/a
39	SRF	chr16:72127355-72127974	ECC-1	luminal epithelium:	n/a	n/a
40	TAF1	chr16:72127491-72128361	H1-neurons	neurons:	n/a	n/a
41	RUNX3	chr16:72127065-72128149	GM12878	blood:	n/a	n/a
42	POLR2A	chr16:72126993-72128337	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr16:72127199-72128431	GM12891	blood:	n/a	n/a
44	POLR2A	chr16:72127124-72128454	GM18505	blood:	n/a	n/a
45	EP300	chr16:72127394-72127897	GM12878	blood:	n/a	chr16:72127492-72127501
46	USF1	chr16:72127346-72127992	ECC-1	luminal epithelium:	n/a	n/a
47	ELK1	chr16:72127225-72127988	GM12878	blood:	n/a	chr16:72127558-72127567 chr16:72127558-72127567
48	ZBTB33	chr16:72127399-72127809	A549	lung:	n/a	n/a
49	REST	chr16:72127148-72128195	HepG2	liver:	n/a	chr16:72127341-72127350 chr16:72127337-72127350 chr16:72127344-72127352
50	MXI1	chr16:72126820-72128414	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153963014..153963707-chr16:72127316..72128049,2	Hela-S3	cervix:
2	chr16:72117553..72119364-chr16:72127046..72129363,2	MCF-7	breast:
3	chr16:72087766..72090367-chr16:72125547..72128434,2	K562	blood:
4	chr16:72099750..72107853-chr16:72126502..72131093,10	MCF-7	breast:
5	chr16:18812518..18813083-chr16:72127604..72128561,3	Hela-S3	cervix:
6	chr16:72042306..72048206-chr16:72125753..72130155,8	MCF-7	breast:
7	chr16:72127015..72130100-chr16:72137516..72139899,4	MCF-7	breast:
8	chr10:28821490..28822049-chr16:72127512..72128106,2	NB4	blood:
9	chr16:72127429..72128033-chr9:140135297..140136119,2	Hela-S3	cervix:
10	chr16:72040983..72044286-chr16:72126039..72129128,5	MCF-7	breast:
11	chr16:72042016..72045516-chr16:72126835..72130601,4	K562	blood:
12	chr16:72127382..72128016-chr18:32621034..32621908,2	HCT-116	colon:
13	chr16:71879510..71881419-chr16:72127750..72129828,2	MCF-7	breast:
14	chr16:72088867..72091285-chr16:72125547..72127887,2	K562	blood:
15	chr11:62358922..62359848-chr16:72127020..72128328,4	Hela-S3	cervix:
16	chr16:71840719..71844104-chr16:72124883..72128411,3	K562	blood:
17	chr11:62609117..62609646-chr16:72127270..72127948,2	NB4	blood:
18	chr16:72127639..72128156-chr17:56736353..56736972,2	Hela-S3	cervix:

Variant related genes	Relation type
TXNL4B	TF binding region
DHX38	TF binding region
ENSG00000095787	Chromatin interaction
ENSG00000254635	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000257017	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000166747	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000224470	Chromatin interaction
ENSG00000260252	Chromatin interaction
ENSG00000166974	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000261701	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000102967	Chromatin interaction
ENSG00000140829	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs57301770	1.00[AMR][1000 genomes]
rs74029816	1.00[AFR][1000 genomes]
rs74029818	1.00[AFR][1000 genomes]
rs74029826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74029843	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak 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	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak 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	58 gene(s)	inside rSNPs	diseases
9	esv1808086	chr16:72088669-72128767	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a
10	esv3343168	chr16:72111500-72128436	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72125800-72128800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr16:72126200-72128400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr16:72126200-72128400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr16:72126200-72128600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr16:72126200-72128600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:72126200-72128800	Active TSS	Ovary	ovary
7	chr16:72126200-72128800	Active TSS	Right Atrium	heart
8	chr16:72126200-72128800	Active TSS	NHLF	lung
9	chr16:72126200-72129000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr16:72126200-72129000	Active TSS	Right Ventricle	heart
11	chr16:72126200-72129000	Active TSS	HSMM	muscle
12	chr16:72126200-72129400	Active TSS	Psoas Muscle	Psoas
13	chr16:72126400-72128000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:72126400-72128600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr16:72126400-72128600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr16:72126400-72128600	Active TSS	Gastric	stomach
17	chr16:72126400-72128800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr16:72126400-72128800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr16:72126400-72128800	Active TSS	Aorta	Aorta
20	chr16:72126400-72128800	Active TSS	Left Ventricle	heart
21	chr16:72126400-72128800	Active TSS	Lung	lung
22	chr16:72126400-72128800	Active TSS	NHDF-Ad	bronchial
23	chr16:72126400-72129000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr16:72126400-72129000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr16:72126400-72129000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:72126600-72128200	Active TSS	Fetal Brain Female	brain
27	chr16:72126600-72128200	Active TSS	Pancreas	Pancrea
28	chr16:72126600-72128400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr16:72126600-72128400	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr16:72126600-72128400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:72126600-72128600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr16:72126600-72128600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr16:72126600-72128600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr16:72126600-72128600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr16:72126600-72128600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr16:72126600-72128600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr16:72126600-72128600	Active TSS	Fetal Intestine Large	intestine
38	chr16:72126600-72128600	Active TSS	Fetal Intestine Small	intestine
39	chr16:72126600-72128600	Active TSS	HSMMtube	muscle
40	chr16:72126600-72128800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:72126600-72128800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:72126600-72128800	Active TSS	A549	lung
43	chr16:72126600-72128800	Active TSS	GM12878-XiMat	blood
44	chr16:72126600-72128800	Bivalent/Poised TSS	HepG2	liver
45	chr16:72126600-72128800	Active TSS	K562	blood
46	chr16:72126600-72129000	Active TSS	H1 Cell Line	embryonic stem cell
47	chr16:72126800-72128200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:72126800-72128200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr16:72126800-72128200	Active TSS	Duodenum Mucosa	Duodenum
50	chr16:72126800-72128200	Active TSS	Fetal Stomach	stomach

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