Variant report

Variant	rs57543641
Chromosome Location	chr3:87042963-87042964
allele	C/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	chr3:87042734-87043366	A549	lung:	n/a	n/a
2	GATA3	chr3:87042535-87043606	A549	lung:	n/a	n/a
3	RCOR1	chr3:87042792-87043315	Hela-S3	cervix:	n/a	n/a
4	FOS	chr3:87042835-87043313	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr3:87042839-87043236	Hela-S3	cervix:	n/a	n/a
6	EP300	chr3:87042673-87043446	A549	lung:	n/a	n/a
7	USF2	chr3:87042697-87043163	Hela-S3	cervix:	n/a	n/a
8	MAX	chr3:87042683-87043496	A549	lung:	n/a	n/a
9	GABPA	chr3:87042747-87043167	A549	lung:	n/a	n/a
10	TCF12	chr3:87042820-87043222	A549	lung:	n/a	n/a
11	CEBPB	chr3:87042839-87043234	IMR90	lung:	n/a	n/a
12	EP300	chr3:87042656-87043505	A549	lung:	n/a	n/a
13	TCF12	chr3:87042489-87043492	A549	lung:	n/a	n/a
14	FOSL2	chr3:87042771-87043226	A549	lung:	n/a	n/a
15	POLR2A	chr3:87042904-87043190	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr3:87042649-87043257	Hela-S3	cervix:	n/a	chr3:87043024-87043033 chr3:87043025-87043034
17	FOS	chr3:87042874-87043191	MCF10A-Er-Src	breast:	n/a	n/a
18	FOXA2	chr3:87042916-87043318	A549	lung:	n/a	n/a
19	JUND	chr3:87042794-87043419	A549	lung:	n/a	n/a
20	FOSL2	chr3:87042609-87043441	A549	lung:	n/a	n/a
21	NR3C1	chr3:87042862-87043262	A549	lung:	n/a	n/a
22	FOS	chr3:87042830-87043210	MCF10A-Er-Src	breast:	n/a	n/a
23	BCL3	chr3:87042705-87043431	A549	lung:	n/a	chr3:87043025-87043034
24	STAT3	chr3:87042928-87043215	MCF10A-Er-Src	breast:	n/a	chr3:87043024-87043033 chr3:87043025-87043034
25	STAT3	chr3:87042919-87043191	MCF10A-Er-Src	breast:	n/a	chr3:87043024-87043033 chr3:87043025-87043034
26	EP300	chr3:87042783-87043394	Hela-S3	cervix:	n/a	n/a
27	JUN	chr3:87042725-87043309	Hela-S3	cervix:	n/a	n/a
28	ELF1	chr3:87042736-87043110	A549	lung:	n/a	chr3:87042957-87042968
29	GATA2	chr3:87042816-87043323	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr3:87042813-87043208	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr3:87042843-87043127	Hela-S3	cervix:	n/a	n/a
32	GABPA	chr3:87042621-87043287	A549	lung:	n/a	n/a
33	CHD2	chr3:87042716-87043282	Hela-S3	cervix:	n/a	n/a
34	ELF1	chr3:87042723-87043269	A549	lung:	n/a	chr3:87042957-87042968
35	GATA3	chr3:87042779-87043447	A549	lung:	n/a	n/a
36	RFX5	chr3:87042867-87043298	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr3:87042452-87043116	MCF10A-Er-Src	breast:	n/a	n/a
38	CEBPB	chr3:87042757-87043312	Hela-S3	cervix:	n/a	n/a
39	FOS	chr3:87042832-87043482	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr3:87042714-87043268	U87	brain:	n/a	n/a
41	SP1	chr3:87042609-87043512	A549	lung:	n/a	n/a
42	POLR2A	chr3:87042553-87043290	U87	brain:	n/a	n/a
43	E2F4	chr3:87042912-87043145	MCF10A-Er-Src	breast:	n/a	n/a
44	TBP	chr3:87042754-87043374	Hela-S3	cervix:	n/a	n/a
45	SP1	chr3:87042652-87043425	A549	lung:	n/a	n/a
46	REST	chr3:87042545-87043401	A549	lung:	n/a	n/a
47	GTF2F1	chr3:87042714-87043326	Hela-S3	cervix:	n/a	n/a
48	RAD21	chr3:87042860-87043325	Hela-S3	cervix:	n/a	n/a
49	KAP1	chr3:87042714-87043330	U2OS	brain:	n/a	n/a
50	POLR2A	chr3:87042547-87043290	U87	brain:	n/a	n/a

Variant related genes	Relation type
VGLL3	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10514743	0.93[ASN][1000 genomes]
rs17028628	0.93[ASN][1000 genomes]
rs1898266	0.93[ASN][1000 genomes]
rs1898267	0.93[ASN][1000 genomes]
rs1898268	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1946747	0.93[ASN][1000 genomes]
rs55854261	0.90[ASN][1000 genomes]
rs56077607	0.96[ASN][1000 genomes]
rs56338126	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56346369	0.96[ASN][1000 genomes]
rs56781488	0.93[ASN][1000 genomes]
rs57070008	0.90[ASN][1000 genomes]
rs57383190	0.90[ASN][1000 genomes]
rs57604593	0.88[ASN][1000 genomes]
rs59090592	0.93[ASN][1000 genomes]
rs59701679	0.96[ASN][1000 genomes]
rs61594756	0.90[ASN][1000 genomes]
rs6551256	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6762893	0.93[ASN][1000 genomes]
rs6763484	0.93[ASN][1000 genomes]
rs6784668	0.93[ASN][1000 genomes]
rs6788077	0.93[ASN][1000 genomes]
rs6802660	0.93[ASN][1000 genomes]
rs72916057	0.88[ASN][1000 genomes]
rs72916059	0.90[ASN][1000 genomes]
rs72916062	0.90[ASN][1000 genomes]
rs72916064	0.90[ASN][1000 genomes]
rs72916069	0.90[ASN][1000 genomes]
rs72916081	0.93[ASN][1000 genomes]
rs72916083	0.93[ASN][1000 genomes]
rs72916086	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72916091	0.93[ASN][1000 genomes]
rs72916092	0.93[ASN][1000 genomes]
rs72916098	0.93[ASN][1000 genomes]
rs72916100	0.93[ASN][1000 genomes]
rs72916102	0.93[ASN][1000 genomes]
rs72918103	0.93[ASN][1000 genomes]
rs72918106	0.93[ASN][1000 genomes]
rs72918107	0.96[ASN][1000 genomes]
rs72918108	0.96[ASN][1000 genomes]
rs72918113	0.96[ASN][1000 genomes]
rs72918116	0.98[ASN][1000 genomes]
rs72918121	0.90[ASN][1000 genomes]
rs72918124	0.90[ASN][1000 genomes]
rs72918169	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73844420	0.90[ASN][1000 genomes]
rs73844421	0.90[ASN][1000 genomes]
rs73844432	0.93[ASN][1000 genomes]
rs73844434	0.93[ASN][1000 genomes]
rs73844442	0.93[ASN][1000 genomes]
rs73844457	0.91[ASN][1000 genomes]
rs7617401	0.87[ASN][1000 genomes]
rs7627441	0.93[ASN][1000 genomes]
rs7645797	0.93[ASN][1000 genomes]
rs7649313	0.93[ASN][1000 genomes]
rs959081	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1000548	chr3:87034157-87331360	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87040800-87044800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:87041000-87043000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:87041000-87043000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:87041000-87043000	Enhancers	Placenta	Placenta
5	chr3:87041000-87043400	Enhancers	NHDF-Ad	bronchial
6	chr3:87041000-87045400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:87041000-87045600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:87041200-87043400	Enhancers	HSMM	muscle
9	chr3:87041200-87043400	Enhancers	NHLF	lung
10	chr3:87041200-87045400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:87041400-87043000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:87041400-87044800	Weak transcription	HMEC	breast
13	chr3:87041400-87046400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:87041800-87044200	Weak transcription	NHEK	skin
15	chr3:87041800-87044800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:87042400-87043200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:87042400-87043400	Enhancers	HUVEC	blood vessel
18	chr3:87042400-87044600	Flanking Active TSS	A549	lung
19	chr3:87042600-87043200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr3:87042600-87043200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:87042600-87043200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:87042600-87043200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:87042600-87043400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:87042600-87043400	Flanking Active TSS	Hela-S3	cervix
25	chr3:87042600-87043400	Flanking Active TSS	NH-A	brain
26	chr3:87042600-87043400	Flanking Active TSS	Osteobl	bone
27	chr3:87042600-87043600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:87042600-87044000	Enhancers	Fetal Lung	lung
29	chr3:87042600-87044400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr3:87042800-87043000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:87042800-87043000	Enhancers	Fetal Intestine Large	intestine
32	chr3:87042800-87043200	Enhancers	Colon Smooth Muscle	Colon
33	chr3:87042800-87043200	Bivalent Enhancer	Fetal Intestine Small	intestine
34	chr3:87042800-87043400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:87042800-87043400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr3:87042800-87043400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:87042800-87043400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:87042800-87043400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:87042800-87043400	Active TSS	Ovary	ovary
40	chr3:87042800-87043400	Flanking Active TSS	HSMMtube	muscle

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