Variant report

Variant	rs1720830
Chromosome Location	chr3:138153206-138153207
allele	G/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	MAX	chr3:138152863-138154146	ECC-1	luminal epithelium:	n/a	chr3:138153304-138153319 chr3:138152991-138153001 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314
2	POLR2A	chr3:138153169-138153848	HepG2	liver:	n/a	n/a
3	USF1	chr3:138153189-138153405	SK-N-SH_RA	brain:	n/a	n/a
4	USF1	chr3:138153166-138153447	HepG2	liver:	n/a	n/a
5	HDAC2	chr3:138153081-138153497	MCF-7	breast:	n/a	n/a
6	E2F6	chr3:138152922-138153982	A549	lung:	n/a	chr3:138153298-138153307
7	GATA3	chr3:138152889-138153465	MCF-7	breast:	n/a	n/a
8	MAX	chr3:138153106-138153641	Hela-S3	cervix:	n/a	chr3:138153304-138153319 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314
9	MYC	chr3:138153150-138153460	MCF10A-Er-Src	breast:	n/a	chr3:138153304-138153319 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314
10	FOXA1	chr3:138153055-138153547	HepG2	liver:	n/a	n/a
11	USF1	chr3:138153172-138153453	A549	lung:	n/a	n/a
12	HA-E2F1	chr3:138152997-138153781	MCF-7	breast:	n/a	chr3:138153298-138153307
13	ELF1	chr3:138153172-138153570	HepG2	liver:	n/a	n/a
14	MYC	chr3:138153084-138153547	HepG2	liver:	n/a	chr3:138153304-138153319 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314
15	USF1	chr3:138153065-138153469	H1-hESC	embryonic stem cell:	n/a	n/a
16	USF1	chr3:138153177-138153403	A549	lung:	n/a	n/a
17	FOXA2	chr3:138153071-138153433	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:138153163-138153682	ECC-1	luminal epithelium:	n/a	n/a
19	CREB1	chr3:138153024-138153764	HepG2	liver:	n/a	n/a
20	FOS	chr3:138153144-138153409	MCF10A-Er-Src	breast:	n/a	chr3:138153233-138153240 chr3:138153231-138153240 chr3:138153370-138153379
21	USF1	chr3:138153143-138153448	SK-N-SH_RA	brain:	n/a	n/a
22	FOSL2	chr3:138153040-138153498	HepG2	liver:	n/a	chr3:138153233-138153240 chr3:138153231-138153240 chr3:138153370-138153379
23	FOXA1	chr3:138153055-138153446	HepG2	liver:	n/a	n/a
24	TAF1	chr3:138153187-138153690	ECC-1	luminal epithelium:	n/a	n/a
25	GABPA	chr3:138153170-138153780	H1-hESC	embryonic stem cell:	n/a	n/a
26	TCF12	chr3:138152975-138153458	A549	lung:	n/a	chr3:138153132-138153139
27	MAX	chr3:138153071-138153738	SK-N-SH	brain:	n/a	chr3:138153304-138153319 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314
28	GABPA	chr3:138152951-138153691	MCF-7	breast:	n/a	n/a
29	GATA3	chr3:138152797-138153808	MCF-7	breast:	n/a	n/a
30	ELF1	chr3:138152924-138153807	MCF-7	breast:	n/a	n/a
31	USF2	chr3:138153155-138153416	Hela-S3	cervix:	n/a	n/a
32	NR2F2	chr3:138152891-138153589	MCF-7	breast:	n/a	n/a
33	MYC	chr3:138153045-138153558	Hela-S3	cervix:	n/a	chr3:138153304-138153319 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314
34	E2F6	chr3:138152669-138154851	H1-hESC	embryonic stem cell:	n/a	chr3:138153298-138153307 chr3:138152832-138152843
35	USF2	chr3:138153196-138153507	H1-hESC	embryonic stem cell:	n/a	n/a
36	NR2F2	chr3:138152972-138153811	MCF-7	breast:	n/a	n/a
37	MXI1	chr3:138153053-138153720	HepG2	liver:	n/a	n/a
38	FOSL2	chr3:138152937-138153443	MCF-7	breast:	n/a	chr3:138153233-138153240 chr3:138153231-138153240 chr3:138153370-138153379
39	E2F6	chr3:138153012-138153684	A549	lung:	n/a	chr3:138153298-138153307
40	POLR2A	chr3:138152674-138153610	K562	blood:	n/a	n/a
41	JUND	chr3:138153092-138153409	HepG2	liver:	n/a	chr3:138153233-138153240 chr3:138153231-138153240 chr3:138153230-138153241 chr3:138153370-138153379
42	ZBTB7A	chr3:138153175-138153807	ECC-1	luminal epithelium:	n/a	n/a
43	MXI1	chr3:138152852-138153831	IMR90	lung:	n/a	n/a
44	GABPA	chr3:138152994-138153722	MCF-7	breast:	n/a	n/a
45	HDAC2	chr3:138153052-138153684	HepG2	liver:	n/a	n/a
46	BHLHE40	chr3:138153202-138153422	HepG2	liver:	n/a	n/a
47	HDAC2	chr3:138152640-138153959	MCF-7	breast:	n/a	chr3:138152798-138152812
48	BHLHE40	chr3:138153048-138153470	HepG2	liver:	n/a	n/a
49	MAX	chr3:138153070-138153704	Hela-S3	cervix:	n/a	chr3:138153304-138153319 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314
50	MAX	chr3:138153041-138153948	HepG2	liver:	n/a	chr3:138153304-138153319 chr3:138153306-138153315 chr3:138153166-138153173 chr3:138153306-138153315 chr3:138153305-138153315 chr3:138153307-138153314

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:138153170-138153220	GM06990	blood:	n/a
2	chr3:138153170-138153220	NHDF-neo	bronchial:	n/a
3	chr3:138153168-138153218	SKMC	muscle:	n/a
4	chr3:138153170-138153220	GM12878	blood:	n/a
5	chr3:138153168-138153218	K562	blood:	n/a
6	chr3:138153170-138153220	MCF-7	breast:	n/a
7	chr3:138153170-138153220	H1-hESC	embryonic stem cell:	embryo
8	chr3:138153168-138153218	CMK	blood:	n/a
9	chr3:138153170-138153220	AoSMC	blood vessel:	n/a
10	chr3:138153168-138153218	SK-N-SH_RA	brain:	n/a
11	chr3:138153168-138153218	AG09309	skin:	n/a
12	chr3:138153168-138153218	A549	lung:	n/a
13	chr3:138153168-138153218	AG10803	skin:	n/a
14	chr3:138153168-138153218	NH-A	brain:	n/a
15	chr3:138153168-138153218	HCM	heart:	n/a
16	chr3:138153168-138153218	GM19239	blood:	n/a
17	chr3:138153170-138153220	ECC-1	luminal epithelium:	n/a
18	chr3:138153168-138153218	HL-60	blood:	n/a
19	chr3:138153168-138153218	HIPEpiC	eye:	n/a
20	chr3:138153168-138153218	GM12891	blood:	n/a
21	chr3:138153168-138153218	HCF	heart:	n/a
22	chr3:138153170-138153220	PFSK-1	brain:	n/a
23	chr3:138153170-138153220	AG10803	skin:	n/a
24	chr3:138153168-138153218	RPTEC	kidney:	n/a
25	chr3:138153170-138153220	Jurkat	blood:	n/a
26	chr3:138153170-138153220	Hela-S3	cervix:	n/a
27	chr3:138153168-138153218	HCT-116	colon:	n/a
28	chr3:138153168-138153218	HPAEpiC	pulmonary alveolar:	n/a
29	chr3:138153170-138153220	Caco-2	colon:	n/a
30	chr3:138153168-138153218	LNCaP	prostate:	n/a
31	chr3:138153168-138153218	HRE	kidney:	n/a
32	chr3:138153168-138153218	NHBE	bronchial:	n/a
33	chr3:138153168-138153218	ProgFib	skin:	n/a
34	chr3:138153170-138153220	SAEC	small airway:	n/a
35	chr3:138153170-138153220	HRPEpiC	eye:	n/a
36	chr3:138153168-138153218	AG04450	lung:	fetal
37	chr3:138153170-138153220	HEK293	kidney:	embryo
38	chr3:138153170-138153220	HCF	heart:	n/a
39	chr3:138153168-138153218	NT2-D1	testis:	n/a
40	chr3:138153170-138153220	SK-N-SH	brain:	n/a
41	chr3:138153168-138153218	AG09319	gingival:	n/a
42	chr3:138153168-138153218	HEK293	kidney:	embryo
43	chr3:138153168-138153218	HEEpiC	esophagus:	n/a
44	chr3:138153170-138153220	HepG2	liver:	n/a
45	chr3:138153170-138153220	HIPEpiC	eye:	n/a
46	chr3:138153168-138153218	PANC-1	pancreas:	n/a
47	chr3:138153170-138153220	GM19239	blood:	n/a
48	chr3:138153170-138153220	AG04449	skin:	fetal
49	chr3:138153170-138153220	ovcar-3	ovarian:	n/a
50	chr3:138153170-138153220	RPTEC	kidney:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138065940..138068792-chr3:138150528..138153476,2	K562	blood:

Variant related genes	Relation type
ESYT3	TF binding region
ESYT3	CpG island
ENSG00000158186	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1109088	0.84[ASN][1000 genomes]
rs12631438	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs12633098	0.87[ASN][1000 genomes]
rs12638938	0.85[ASN][1000 genomes]
rs1403776	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1403777	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1546758	0.88[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs1679153	0.94[CHB][hapmap];0.97[CHD][hapmap]
rs1679170	0.85[ASN][1000 genomes]
rs1679176	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679177	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679179	0.87[ASN][1000 genomes]
rs1679181	0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[ASN][1000 genomes]
rs171693	1.00[EUR][1000 genomes]
rs1720826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720829	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs1720832	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305269	1.00[TSI][hapmap]
rs34963112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775027	0.90[EUR][1000 genomes]
rs7609893	0.84[ASN][1000 genomes]
rs7611650	0.84[ASN][1000 genomes]
rs774013	0.82[ASN][1000 genomes]
rs774014	0.85[ASN][1000 genomes]
rs774374	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs809573	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs812277	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs940234	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138152200-138155000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:138152400-138154800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:138152600-138153600	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr3:138152600-138153800	Bivalent Enhancer	Fetal Thymus	thymus
5	chr3:138152600-138154000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:138152600-138154600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:138152600-138154800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr3:138152600-138154800	Active TSS	Brain Angular Gyrus	brain
9	chr3:138152800-138153400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
10	chr3:138152800-138153400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:138152800-138153400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
12	chr3:138152800-138153400	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr3:138152800-138153400	Bivalent Enhancer	Placenta	Placenta
14	chr3:138152800-138153400	Enhancers	Spleen	Spleen
15	chr3:138152800-138153400	ZNF genes & repeats	HSMM	muscle
16	chr3:138152800-138153600	Enhancers	Primary hematopoietic stem cells	blood
17	chr3:138152800-138153800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
18	chr3:138152800-138153800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr3:138152800-138153800	Active TSS	Brain Substantia Nigra	brain
20	chr3:138152800-138154200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:138152800-138154400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr3:138152800-138154400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:138152800-138154400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:138152800-138154400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:138152800-138154400	Active TSS	Aorta	Aorta
26	chr3:138152800-138154600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:138152800-138154600	Bivalent Enhancer	Fetal Brain Male	brain
28	chr3:138152800-138154600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr3:138152800-138154800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:138153000-138153400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:138153000-138153400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
33	chr3:138153000-138153400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:138153000-138153400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:138153000-138153400	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr3:138153000-138153400	Bivalent/Poised TSS	Fetal Kidney	kidney
38	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
39	chr3:138153000-138153400	Enhancers	Gastric	stomach
40	chr3:138153000-138153400	Flanking Active TSS	Left Ventricle	heart
41	chr3:138153000-138153400	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
43	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
44	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	Thymus	Thymus
45	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	HepG2	liver
46	chr3:138153000-138153400	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
47	chr3:138153000-138153600	Enhancers	Fetal Heart	heart
48	chr3:138153000-138153600	Flanking Active TSS	Lung	lung
49	chr3:138153000-138153600	Flanking Active TSS	Ovary	ovary
50	chr3:138153000-138153800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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