Variant report

Variant	rs73890713
Chromosome Location	chr3:194908320-194908321
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	MYC	chr3:194908288-194908719	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:194908306-194908664	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:194908252-194908813	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:194908285-194908839	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:194908290-194908844	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr3:194908289-194909095	MCF10A-Er-Src	breast:	n/a	chr3:194908565-194908574 chr3:194908560-194908580 chr3:194908563-194908577 chr3:194908564-194908575 chr3:194908566-194908575
7	POLR2A	chr3:194908232-194909337	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr3:194908240-194909027	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:194905664..194908891-chr3:194914398..194916423,3	K562	blood:
2	chr3:194897295..194902185-chr3:194905804..194909141,6	K562	blood:
3	chr3:194906722..194908372-chr3:194922771..194924714,2	MCF-7	breast:
4	chr3:194906815..194911611-chr3:194916675..194920611,6	K562	blood:
5	chr3:194897295..194902438-chr3:194905804..194908922,5	K562	blood:
6	chr3:194886082..194888660-chr3:194907864..194909692,2	K562	blood:
7	chr3:194903828..194906492-chr3:194907226..194909497,3	K562	blood:

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs35136713	1.00[AMR][1000 genomes]
rs56386553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61422283	1.00[AMR][1000 genomes]
rs6773392	1.00[AMR][1000 genomes]
rs6789088	1.00[AMR][1000 genomes]
rs6806859	1.00[AMR][1000 genomes]
rs6809483	1.00[AMR][1000 genomes]
rs73067087	1.00[AMR][1000 genomes]
rs73890627	1.00[AMR][1000 genomes]
rs73890636	1.00[AMR][1000 genomes]
rs73890648	1.00[AMR][1000 genomes]
rs73890650	1.00[AMR][1000 genomes]
rs73890665	1.00[AMR][1000 genomes]
rs73890666	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
12	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
13	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
14	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194884800-194908800	Weak transcription	Thymus	Thymus
2	chr3:194896600-194909200	Weak transcription	Pancreas	Pancrea
3	chr3:194901200-194908600	Weak transcription	Fetal Heart	heart
4	chr3:194901600-194909000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:194903000-194909000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:194903000-194909000	Weak transcription	Ovary	ovary
7	chr3:194903000-194915200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:194903200-194909000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:194903200-194909000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:194903200-194915000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:194903400-194908600	Weak transcription	HSMM	muscle
12	chr3:194903600-194908800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:194903600-194909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:194903600-194909000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:194903800-194908600	Enhancers	Colon Smooth Muscle	Colon
16	chr3:194903800-194908800	Weak transcription	Fetal Kidney	kidney
17	chr3:194904000-194908800	Weak transcription	Fetal Brain Female	brain
18	chr3:194904200-194908400	Weak transcription	Fetal Lung	lung
19	chr3:194904400-194908400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:194904600-194908400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:194904600-194916400	Weak transcription	Right Atrium	heart
22	chr3:194904800-194908600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:194905000-194908800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:194905600-194909000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:194905600-194909600	Enhancers	Placenta	Placenta
26	chr3:194905600-194910000	Enhancers	K562	blood
27	chr3:194905800-194908400	Enhancers	NHEK	skin
28	chr3:194905800-194909600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:194906000-194908400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:194906000-194908400	Enhancers	NHDF-Ad	bronchial
31	chr3:194906000-194909400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:194906000-194909400	Enhancers	Stomach Smooth Muscle	stomach
33	chr3:194906000-194909800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:194906000-194909800	Enhancers	HMEC	breast
35	chr3:194906200-194908400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:194906400-194908400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:194906400-194908400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:194906400-194909600	Enhancers	GM12878-XiMat	blood
39	chr3:194906800-194909800	Enhancers	HepG2	liver
40	chr3:194907000-194908400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:194907000-194908800	Weak transcription	Adipose Nuclei	Adipose
42	chr3:194907200-194911000	Weak transcription	Lung	lung
43	chr3:194907400-194908400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:194907400-194908400	Weak transcription	Stomach Mucosa	stomach
45	chr3:194907400-194908400	Enhancers	NHLF	lung
46	chr3:194907400-194908800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:194907400-194908800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:194907400-194909000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:194907400-194909000	Weak transcription	Psoas Muscle	Psoas
50	chr3:194907400-194909200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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