Variant report

Variant	rs41461744
Chromosome Location	chr3:46205022-46205023
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	ELF1	chr3:46204946-46205544	MCF-7	breast:	n/a	n/a
2	MAFK	chr3:46204661-46205350	H1-hESC	embryonic stem cell:	n/a	chr3:46204890-46204905
3	FOS	chr3:46204758-46205517	MCF10A-Er-Src	breast:	n/a	n/a
4	NR3C1	chr3:46204760-46205046	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:46204791-46205163	MCF10A-Er-Src	breast:	n/a	n/a
6	ESR1	chr3:46204482-46205081	T-47D	breast:	n/a	chr3:46204649-46204664 chr3:46204670-46204685
7	GTF2F1	chr3:46204835-46205368	Hela-S3	cervix:	n/a	n/a
8	GATA3	chr3:46204535-46205664	MCF-7	breast:	n/a	n/a
9	FOS	chr3:46204715-46205560	MCF10A-Er-Src	breast:	n/a	n/a
10	BACH1	chr3:46204630-46205317	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr3:46204570-46205713	MCF-7	breast:	n/a	n/a
12	POLR2A	chr3:46204978-46205039	MCF-7	breast:	n/a	n/a
13	MAZ	chr3:46204830-46205327	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr3:46204389-46205125	ECC-1	luminal epithelium:	n/a	n/a
15	SIN3AK20	chr3:46204571-46205441	MCF-7	breast:	n/a	n/a
16	FOSL1	chr3:46204481-46205458	HCT-116	colon:	n/a	n/a
17	MAX	chr3:46204790-46205543	Hela-S3	cervix:	n/a	n/a
18	JUND	chr3:46204840-46205071	K562	blood:	n/a	n/a
19	ESR1	chr3:46204423-46205046	T-47D	breast:	n/a	chr3:46204649-46204664 chr3:46204670-46204685
20	EP300	chr3:46204601-46205685	T-47D	breast:	n/a	n/a
21	JUND	chr3:46204566-46205420	MCF-7	breast:	n/a	n/a
22	NR2F2	chr3:46204597-46205197	MCF-7	breast:	n/a	n/a
23	MAX	chr3:46204669-46205623	MCF-7	breast:	n/a	n/a
24	GATA3	chr3:46204501-46205737	MCF-7	breast:	n/a	n/a
25	NR2F2	chr3:46204494-46205616	MCF-7	breast:	n/a	n/a
26	POLR2A	chr3:46204856-46205368	MCF-7	breast:	n/a	n/a
27	JUND	chr3:46204758-46205495	MCF-7	breast:	n/a	n/a
28	RAD21	chr3:46204400-46205053	MCF-7	breast:	n/a	n/a
29	TCF12	chr3:46204542-46205388	ECC-1	luminal epithelium:	n/a	n/a
30	GATA3	chr3:46204603-46205718	T-47D	breast:	n/a	n/a
31	EP300	chr3:46204401-46205582	MCF-7	breast:	n/a	n/a
32	JUND	chr3:46204605-46205707	T-47D	breast:	n/a	n/a
33	FOSL2	chr3:46204752-46205050	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:46204706-46205313	MCF10A-Er-Src	breast:	n/a	n/a
35	MAFK	chr3:46204702-46205341	Hela-S3	cervix:	n/a	chr3:46204890-46204905
36	FOSL2	chr3:46204655-46205463	MCF-7	breast:	n/a	n/a
37	POLR2A	chr3:46204947-46205116	MCF-7	breast:	n/a	n/a
38	ESR1	chr3:46204450-46205539	T-47D	breast:	n/a	chr3:46204649-46204664 chr3:46204670-46204685
39	CEBPB	chr3:46204700-46205585	Hela-S3	cervix:	n/a	n/a
40	ESR1	chr3:46204400-46205116	T-47D	breast:	n/a	chr3:46204649-46204664 chr3:46204670-46204685
41	TEAD4	chr3:46204642-46205454	ECC-1	luminal epithelium:	n/a	n/a
42	CHD2	chr3:46204804-46205089	Hela-S3	cervix:	n/a	n/a
43	TCF7L2	chr3:46204706-46205443	MCF-7	breast:	n/a	n/a
44	STAT3	chr3:46204771-46205482	MCF10A-Er-Src	breast:	n/a	n/a
45	TFAP2C	chr3:46204751-46205531	Hela-S3	cervix:	n/a	n/a
46	ZKSCAN1	chr3:46204798-46205090	Hela-S3	cervix:	n/a	n/a
47	GATA3	chr3:46204716-46205659	T-47D	breast:	n/a	n/a
48	RAD21	chr3:46204500-46205459	Hela-S3	cervix:	n/a	n/a
49	JUND	chr3:46204528-46205467	HCT-116	colon:	n/a	n/a
50	EP300	chr3:46204580-46205504	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46202705..46205195-chr3:46247195..46250047,2	MCF-7	breast:

Variant related genes	Relation type
CCR3	TF binding region
ENSG00000163823	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510749	0.82[AFR][1000 genomes]
rs13083914	0.84[AFR][1000 genomes]
rs13084057	0.84[AFR][1000 genomes]
rs13084175	0.84[AFR][1000 genomes]
rs17078660	0.91[AFR][1000 genomes]
rs17078695	0.96[AFR][1000 genomes]
rs34401473	0.84[AFR][1000 genomes]
rs41326147	0.86[AFR][1000 genomes]
rs41366344	0.86[AFR][1000 genomes]
rs41406247	1.00[AFR][1000 genomes]
rs41424051	0.86[AFR][1000 genomes]
rs41465848	0.82[AFR][1000 genomes]
rs41480548	0.82[AFR][1000 genomes]
rs6793690	0.81[AFR][1000 genomes]
rs902761	0.85[AFR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46202600-46205400	Weak transcription	Thymus	Thymus
2	chr3:46202800-46206200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:46203400-46205400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:46203600-46205200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:46203600-46205400	Enhancers	HepG2	liver
6	chr3:46203600-46206200	Enhancers	Placenta	Placenta
7	chr3:46203800-46205400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:46204000-46205400	Enhancers	Esophagus	oesophagus
9	chr3:46204000-46205400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:46204000-46206000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:46204400-46205200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:46204400-46205600	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr3:46204400-46205800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:46204400-46205800	Enhancers	Fetal Thymus	thymus
15	chr3:46204400-46205800	Enhancers	Lung	lung
16	chr3:46204400-46206000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:46204600-46205200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:46204600-46205400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:46204600-46205600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:46204600-46205800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:46204600-46205800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr3:46204600-46205800	Flanking Active TSS	NHEK	skin
23	chr3:46204800-46205200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr3:46204800-46205200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:46204800-46205200	Enhancers	HSMM	muscle
26	chr3:46204800-46205200	Enhancers	HSMMtube	muscle
27	chr3:46204800-46205400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:46204800-46205400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:46204800-46205800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:46204800-46205800	Flanking Active TSS	Hela-S3	cervix
31	chr3:46204800-46205800	Flanking Active TSS	HMEC	breast
32	chr3:46205000-46205400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr3:46205000-46205600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:46205000-46205800	Enhancers	Fetal Lung	lung

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