Variant report

Variant	rs4958984
Chromosome Location	chr5:177366226-177366227
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	chr5:177366085-177366881	MCF-7	breast:	n/a	n/a
2	POLR2A	chr5:177366122-177366921	MCF-7	breast:	n/a	n/a
3	HA-E2F1	chr5:177366104-177366708	MCF-7	breast:	n/a	n/a
4	POLR2A	chr5:177366220-177366609	ECC-1	luminal epithelium:	n/a	n/a
5	MXI1	chr5:177366212-177366804	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:177366175-177366284	HepG2	liver:	n/a	n/a
7	MYC	chr5:177366202-177366939	MCF-7	breast:	n/a	n/a
8	MYC	chr5:177366191-177366320	MCF-7	breast:	n/a	n/a
9	POLR2A	chr5:177366151-177366885	A549	lung:	n/a	n/a
10	POLR2A	chr5:177366153-177366888	MCF-7	breast:	n/a	n/a
11	POLR2A	chr5:177366193-177366802	A549	lung:	n/a	n/a
12	POLR2A	chr5:177366194-177366853	ProgFib	skin:	n/a	n/a
13	POLR2A	chr5:177366130-177366794	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000250101	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10464113	0.81[ASN][1000 genomes]
rs11738026	0.82[ASN][1000 genomes]
rs11740972	0.81[AFR][1000 genomes]
rs4246052	0.81[ASN][1000 genomes]
rs4318803	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4318804	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4327608	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4428434	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4958942	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958944	0.82[ASN][1000 genomes]
rs4958980	0.83[AFR][1000 genomes]
rs4958982	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4958983	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4958991	0.82[ASN][1000 genomes]
rs4958992	0.86[ASN][1000 genomes]
rs62397830	0.80[ASN][1000 genomes]
rs6601187	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6601188	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6864280	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6866295	0.85[ASN][1000 genomes]
rs6875120	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6875636	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6880829	0.87[AFR][1000 genomes]
rs6881018	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6891157	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7703493	0.83[ASN][1000 genomes]
rs9764398	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9765519	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
2	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription 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	78 gene(s)	inside rSNPs	diseases
3	nsv1033211	chr5:177133646-177383386	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv883184	chr5:177311043-177488281	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv883185	chr5:177357964-177401509	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv521629	chr5:177364884-177396200	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3377185	chr5:177365371-177368219	Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177365600-177366400	Enhancers	Primary B cells from peripheral blood	blood
2	chr5:177365600-177366800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:177365600-177366800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:177365600-177366800	Enhancers	Primary B cells from cord blood	blood
5	chr5:177365600-177367000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:177365600-177368200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:177365800-177366400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:177365800-177366400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:177365800-177366400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:177365800-177366400	Enhancers	Fetal Lung	lung
11	chr5:177365800-177366600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr5:177365800-177367000	Active TSS	Brain Germinal Matrix	brain
13	chr5:177365800-177367200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr5:177365800-177367200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:177365800-177367200	Active TSS	Muscle Satellite Cultured Cells	--
16	chr5:177365800-177367200	Bivalent Enhancer	Fetal Thymus	thymus
17	chr5:177365800-177367400	Active TSS	NHLF	lung
18	chr5:177366000-177366400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
19	chr5:177366000-177366400	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr5:177366000-177366600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:177366000-177366600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:177366000-177366800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr5:177366000-177366800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:177366000-177366800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:177366000-177366800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:177366000-177366800	Active TSS	Duodenum Mucosa	Duodenum
27	chr5:177366000-177366800	Active TSS	HSMMtube	muscle
28	chr5:177366000-177367000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr5:177366000-177367000	Active TSS	HMEC	breast
30	chr5:177366000-177367000	Active TSS	Osteobl	bone
31	chr5:177366000-177367200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:177366000-177367200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:177366000-177367200	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr5:177366000-177367200	Active TSS	A549	lung
35	chr5:177366000-177367200	Active TSS	HSMM	muscle
36	chr5:177366000-177367200	Active TSS	NHDF-Ad	bronchial
37	chr5:177366000-177371200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:177366200-177366400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:177366200-177366400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:177366200-177366400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr5:177366200-177366400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr5:177366200-177366400	Active TSS	Fetal Intestine Small	intestine
43	chr5:177366200-177366400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr5:177366200-177366400	Active TSS	Gastric	stomach
45	chr5:177366200-177366400	Enhancers	Lung	lung
46	chr5:177366200-177366400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr5:177366200-177366600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:177366200-177366600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr5:177366200-177366600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:177366200-177366600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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