Variant report

Variant	rs66570007
Chromosome Location	chr3:196296320-196296321
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	SIN3AK20	chr3:196295079-196296388	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr3:196295912-196296363	H1-neurons	neurons:	n/a	n/a
3	HCFC1	chr3:196293701-196297089	Hela-S3	cervix:	n/a	n/a
4	UBTF	chr3:196295088-196296545	K562	blood:	n/a	n/a
5	E2F1	chr3:196295164-196296393	Hela-S3	cervix:	n/a	n/a
6	TFAP2A	chr3:196295294-196296457	Hela-S3	cervix:	n/a	chr3:196296181-196296192 chr3:196295431-196295442 chr3:196296182-196296190 chr3:196296182-196296190 chr3:196296182-196296190
7	SIN3A	chr3:196294917-196296502	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:196294890-196296373	K562	blood:	n/a	n/a
9	POLR2A	chr3:196295103-196296381	ProgFib	skin:	n/a	n/a
10	ELF1	chr3:196296187-196296504	K562	blood:	n/a	chr3:196296374-196296385 chr3:196296373-196296386
11	POLR2A	chr3:196294993-196296344	MCF-7	breast:	n/a	n/a
12	REST	chr3:196295934-196296358	ECC-1	luminal epithelium:	n/a	chr3:196296210-196296220
13	MAX	chr3:196294721-196296371	ECC-1	luminal epithelium:	n/a	chr3:196295552-196295561
14	RFX5	chr3:196296045-196296337	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:196295910-196296461	Hela-S3	cervix:	n/a	n/a
16	YY1	chr3:196294974-196296362	K562	blood:	n/a	chr3:196296193-196296204
17	MTA3	chr3:196295931-196296555	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:196294714-196296360	GM12892	blood:	n/a	n/a
19	TAF1	chr3:196295928-196296410	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr3:196294489-196296572	IMR90	lung:	n/a	n/a
21	TBP	chr3:196294880-196296351	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr3:196295074-196296354	ECC-1	luminal epithelium:	n/a	chr3:196296193-196296204
23	POLR2A	chr3:196293763-196296428	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:196295927-196296440	K562	blood:	n/a	n/a
25	UBTF	chr3:196295358-196296496	K562	blood:	n/a	n/a
26	SMARCB1	chr3:196294993-196296332	Hela-S3	cervix:	n/a	n/a
27	HEY1	chr3:196295938-196296335	K562	blood:	n/a	n/a
28	E2F4	chr3:196296086-196296394	MCF10A-Er-Src	breast:	n/a	n/a
29	CHD2	chr3:196296090-196296371	Hela-S3	cervix:	n/a	chr3:196296311-196296321
30	POLR2A	chr3:196295895-196296345	GM12878	blood:	n/a	n/a
31	MAX	chr3:196295941-196296369	A549	lung:	n/a	n/a
32	CREB1	chr3:196294871-196296399	HepG2	liver:	n/a	chr3:196294884-196294897
33	SIN3AK20	chr3:196294836-196296599	MCF-7	breast:	n/a	n/a
34	POLR2A	chr3:196295000-196296351	GM12892	blood:	n/a	n/a
35	TAF1	chr3:196295920-196296358	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:196295930-196296425	Hela-S3	cervix:	n/a	n/a
37	MAZ	chr3:196296223-196296347	K562	blood:	n/a	n/a
38	JUN	chr3:196294719-196297220	K562	blood:	n/a	chr3:196296209-196296218 chr3:196295398-196295407
39	TFAP2C	chr3:196295174-196296440	Hela-S3	cervix:	n/a	chr3:196296177-196296192
40	MAZ	chr3:196295078-196296560	IMR90	lung:	n/a	chr3:196295552-196295561
41	E2F4	chr3:196295159-196296326	Hela-S3	cervix:	n/a	chr3:196295393-196295404
42	POLR2A	chr3:196295061-196296320	H1-hESC	embryonic stem cell:	n/a	n/a
43	HA-E2F1	chr3:196294883-196296453	MCF-7	breast:	n/a	chr3:196296434-196296448
44	YY1	chr3:196295101-196296389	HepG2	liver:	n/a	chr3:196296193-196296204
45	MXI1	chr3:196295987-196296437	Hela-S3	cervix:	n/a	n/a
46	ELF1	chr3:196294959-196296338	GM12878	blood:	n/a	n/a
47	TAF1	chr3:196294925-196296343	ECC-1	luminal epithelium:	n/a	n/a
48	MXI1	chr3:196294448-196297042	SK-N-SH	brain:	n/a	n/a
49	MAX	chr3:196295912-196296436	K562	blood:	n/a	n/a
50	POLR2A	chr3:196294323-196296379	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196294811..196297703-chr3:196694216..196696736,3	K562	blood:
2	chr3:196292428..196296416-chr3:196668494..196671676,5	MCF-7	breast:
3	chr3:196253926..196256027-chr3:196295277..196297106,2	K562	blood:
4	chr3:196294271..196297444-chr3:196668008..196671102,3	K562	blood:
5	chr3:196228489..196231887-chr3:196292830..196296417,3	MCF-7	breast:
6	chr3:196294271..196297444-chr3:196668008..196671102,4	K562	blood:
7	chr3:196294935..196297677-chr3:196667748..196670021,2	MCF-7	breast:
8	chr3:196295234..196297248-chr3:196695881..196697586,3	MCF-7	breast:
9	chr3:196294586..196296980-chr3:196730003..196731682,2	MCF-7	breast:
10	chr3:196295485..196297090-chr3:196694773..196696786,2	MCF-7	breast:
11	chr3:196293733..196296360-chr3:196359092..196361282,2	MCF-7	breast:
12	chr3:196228351..196232071-chr3:196294107..196297178,4	MCF-7	breast:

Variant related genes	Relation type
WDR53	TF binding region
ENSG00000114503	Chromatin interaction
ENSG00000270170	Chromatin interaction
ENSG00000213358	Chromatin interaction
ENSG00000232065	Chromatin interaction
ENSG00000228109	Chromatin interaction
ENSG00000163975	Chromatin interaction
ENSG00000119227	Chromatin interaction
ENSG00000163961	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11185546	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12485589	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634928	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12636646	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12636666	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1872353	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2341337	0.86[EUR][1000 genomes]
rs34676641	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35827219	0.87[EUR][1000 genomes]
rs6764637	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6791472	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808029	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648453	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs970414	0.95[AMR][1000 genomes]
rs9870529	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	esv3347483	chr3:196294955-196297053	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196294000-196296400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:196294200-196296600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:196294200-196296600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:196294200-196296800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:196294200-196297000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:196294400-196296600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr3:196294400-196296800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:196294400-196296800	Active TSS	Right Ventricle	heart
9	chr3:196294400-196296800	Active TSS	HSMM	muscle
10	chr3:196294400-196297000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr3:196294400-196297000	Active TSS	A549	lung
12	chr3:196294400-196297200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:196294600-196296400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr3:196294600-196296400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:196294600-196296400	Active TSS	K562	blood
16	chr3:196294600-196296600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:196294600-196296600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:196294600-196296600	Active TSS	Placenta Amnion	Placenta Amnion
19	chr3:196294600-196296800	Active TSS	Small Intestine	intestine
20	chr3:196294600-196297000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:196294800-196296400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr3:196294800-196296400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:196294800-196296400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:196294800-196296400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:196294800-196296400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:196294800-196296400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:196294800-196296400	Active TSS	Muscle Satellite Cultured Cells	--
28	chr3:196294800-196296400	Active TSS	Brain Hippocampus Middle	brain
29	chr3:196294800-196296400	Active TSS	Fetal Intestine Small	intestine
30	chr3:196294800-196296400	Active TSS	Gastric	stomach
31	chr3:196294800-196296400	Active TSS	Pancreas	Pancrea
32	chr3:196294800-196296400	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr3:196294800-196296600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr3:196294800-196296600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:196294800-196296600	Active TSS	Aorta	Aorta
36	chr3:196294800-196296600	Active TSS	Fetal Kidney	kidney
37	chr3:196294800-196296600	Active TSS	Ovary	ovary
38	chr3:196294800-196296600	Active TSS	Right Atrium	heart
39	chr3:196294800-196296600	Active TSS	HMEC	breast
40	chr3:196294800-196296600	Active TSS	NHDF-Ad	bronchial
41	chr3:196294800-196296800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr3:196294800-196296800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:196294800-196296800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:196294800-196296800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:196294800-196296800	Active TSS	Fetal Intestine Large	intestine
46	chr3:196294800-196296800	Active TSS	Left Ventricle	heart
47	chr3:196294800-196296800	Active TSS	Psoas Muscle	Psoas
48	chr3:196294800-196296800	Active TSS	GM12878-XiMat	blood
49	chr3:196294800-196296800	Active TSS	NHLF	lung
50	chr3:196294800-196297200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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