Variant report

Variant	rs1915365
Chromosome Location	chr3:150479070-150479071
allele	C/G
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	POLR2A	chr3:150476883-150483109	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:150477871-150479157	K562	blood:	n/a	n/a
3	POLR2A	chr3:150478964-150483373	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:150479014-150480086	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:150478870-150479135	MCF-7	breast:	n/a	n/a
6	MTA3	chr3:150477787-150479126	GM12878	blood:	n/a	n/a
7	MXI1	chr3:150477822-150483051	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr3:150477904-150479143	GM12878	blood:	n/a	n/a
9	TBP	chr3:150478028-150479324	GM12878	blood:	n/a	chr3:150478721-150478732
10	MTA3	chr3:150478031-150479530	GM12878	blood:	n/a	n/a
11	EBF1	chr3:150478038-150479189	GM12878	blood:	n/a	chr3:150478369-150478380
12	POLR2A	chr3:150477211-150480410	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:150477065-150480316	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:150476896-150484835	GM12878	blood:	n/a	n/a
15	MXI1	chr3:150478984-150482211	IMR90	lung:	n/a	n/a
16	POLR2A	chr3:150478967-150480433	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:150476950-150483136	PBDE	blood:	n/a	n/a
18	POLR2A	chr3:150479029-150479229	MCF10A-Er-Src	breast:	n/a	n/a
19	CHD1	chr3:150477878-150482271	GM12878	blood:	n/a	n/a
20	HEY1	chr3:150479035-150479306	HepG2	liver:	n/a	n/a
21	STAT3	chr3:150478164-150479242	GM12878	blood:	n/a	chr3:150478231-150478239 chr3:150478228-150478242 chr3:150478229-150478240 chr3:150478323-150478334
22	POLR2A	chr3:150478773-150479176	MCF10A-Er-Src	breast:	n/a	n/a
23	IRF1	chr3:150478932-150479880	K562	blood:	n/a	chr3:150479434-150479455

No.	Distal block	Cell Line	Cell type
1	chr3:150263797..150265530-chr3:150478854..150481327,3	MCF-7	breast:
2	chr3:150319354..150323687-chr3:150477863..150484487,11	MCF-7	breast:
3	chr3:150261800..150265866-chr3:150477764..150484308,7	MCF-7	breast:
4	chr3:150125257..150128558-chr3:150478258..150482422,4	K562	blood:
5	chr3:150433681..150449199-chr3:150473254..150487048,35	MCF-7	breast:

Variant related genes	Relation type
SIAH2-AS1	TF binding region
ENSG00000144895	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000244668	Chromatin interaction
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1373418	0.81[EUR][1000 genomes]
rs1444197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16862842	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1814463	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1814464	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1838337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1879420	0.83[AMR][1000 genomes]
rs2014279	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2018246	0.81[EUR][1000 genomes]
rs2116684	0.83[AMR][1000 genomes]
rs2120596	0.88[AMR][1000 genomes]
rs2869479	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34348847	0.81[EUR][1000 genomes]
rs34771595	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3851356	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41354246	0.81[EUR][1000 genomes]
rs41372346	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41454348	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56840421	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57278175	0.93[EUR][1000 genomes]
rs57359526	0.83[AMR][1000 genomes]
rs57869178	0.81[EUR][1000 genomes]
rs57965761	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58403524	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58418105	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60092981	0.88[AMR][1000 genomes]
rs60259684	0.81[EUR][1000 genomes]
rs60523415	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60538652	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61628582	0.83[AMR][1000 genomes]
rs6440696	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6440697	0.81[EUR][1000 genomes]
rs6440698	0.81[EUR][1000 genomes]
rs6769917	0.81[EUR][1000 genomes]
rs6777178	0.81[EUR][1000 genomes]
rs6795396	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6803830	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6805481	0.81[EUR][1000 genomes]
rs6806197	0.93[EUR][1000 genomes]
rs71764080	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72993403	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73003787	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73003792	0.81[EUR][1000 genomes]
rs73006998	0.85[EUR][1000 genomes]
rs73010941	0.81[EUR][1000 genomes]
rs73010947	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73010956	0.81[EUR][1000 genomes]
rs73010964	0.81[EUR][1000 genomes]
rs73010965	0.81[EUR][1000 genomes]
rs73010967	1.00[EUR][1000 genomes]
rs73869297	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7615125	0.85[EUR][1000 genomes]
rs7615292	0.85[EUR][1000 genomes]
rs7617507	0.81[EUR][1000 genomes]
rs7628481	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628776	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv592035	chr3:150478018-150481021	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	nsv592036	chr3:150478018-150481236	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	n/a
4	esv1820145	chr3:150478018-150487945	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3420624	chr3:150478562-150482960	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150471200-150479600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:150471600-150479600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:150475000-150479800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr3:150475400-150480400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:150477000-150479400	Flanking Active TSS	Liver	Liver
6	chr3:150477000-150479400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:150477200-150479800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr3:150477200-150480400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr3:150477400-150480000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:150477600-150479200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:150477600-150479200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr3:150477600-150479200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr3:150477600-150479200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:150477600-150479600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:150477600-150479600	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr3:150477600-150479800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:150477600-150480200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:150477600-150480400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr3:150477800-150479400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr3:150477800-150479400	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr3:150477800-150479400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr3:150477800-150479400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr3:150477800-150479400	Flanking Active TSS	HUVEC	blood vessel
24	chr3:150477800-150479400	Flanking Active TSS	Osteobl	bone
25	chr3:150477800-150479600	Weak transcription	Gastric	stomach
26	chr3:150477800-150479800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr3:150477800-150479800	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr3:150477800-150480000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr3:150478000-150479200	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr3:150478000-150479200	Flanking Active TSS	NH-A	brain
31	chr3:150478000-150479400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr3:150478000-150479400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:150478000-150479400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr3:150478000-150479400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr3:150478000-150479600	Weak transcription	Spleen	Spleen
36	chr3:150478000-150479800	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr3:150478000-150479800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr3:150478000-150480000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr3:150478000-150482000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:150478000-150482200	Active TSS	Thymus	Thymus
41	chr3:150478200-150479200	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr3:150478200-150479200	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr3:150478200-150479200	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr3:150478200-150479200	Flanking Active TSS	A549	lung
45	chr3:150478200-150479200	Flanking Active TSS	NHEK	skin
46	chr3:150478200-150479400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:150478200-150479400	Flanking Active TSS	Fetal Brain Female	brain
48	chr3:150478200-150479600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:150478200-150479600	Flanking Active TSS	Fetal Brain Male	brain
50	chr3:150478200-150479600	Weak transcription	Lung	lung

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