Variant report

Variant	rs248253
Chromosome Location	chr5:179287597-179287598
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179287562-179287677	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr5:179287267-179287622	HCT-116	colon:	n/a	n/a
3	POLR2A	chr5:179285251-179287664	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:179287242-179287760	U87	brain:	n/a	n/a
5	EP300	chr5:179287427-179287643	K562	blood:	n/a	n/a
6	POLR2A	chr5:179286683-179287632	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr5:179286666-179287682	PANC-1	pancreas:	n/a	n/a
8	BACH1	chr5:179287475-179287705	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179246365..179250489-chr5:179281961..179288216,8	MCF-7	breast:
2	chr5:179262940..179266304-chr5:179284329..179288957,4	K562	blood:
3	chr5:179124684..179126939-chr5:179285490..179289046,3	MCF-7	breast:
4	chr5:179227703..179229883-chr5:179285735..179288229,2	K562	blood:
5	chr5:179245762..179250347-chr5:179281858..179288397,17	MCF-7	breast:
6	chr5:179285948..179288985-chr5:179497401..179500729,4	K562	blood:
7	chr5:179285279..179287519-chr5:179287534..179289534,3	MCF-7	breast:
8	chr5:179244299..179249031-chr5:179283718..179288072,6	K562	blood:
9	chr5:179227703..179229883-chr5:179285735..179289127,3	K562	blood:
10	chr5:179280059..179282824-chr5:179286151..179287699,2	K562	blood:
11	chr5:179285987..179287986-chr5:179498943..179500555,2	K562	blood:
12	chr5:179286272..179289158-chr5:179311658..179315263,3	K562	blood:
13	chr5:179287101..179289302-chr5:179295168..179298855,3	K562	blood:
14	chr5:179249726..179253531-chr5:179284409..179289652,9	K562	blood:
15	chr5:179285301..179288103-chr5:179290972..179294711,5	MCF-7	breast:
16	chr5:179232940..179234909-chr5:179286126..179288451,2	K562	blood:
17	chr5:179284411..179288482-chr5:179291303..179294641,8	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D9B-1	chr5:179287514-179287707	NONHSAT105649

No data

Variant related genes	Relation type
C5orf45	TF binding region
ENSG00000245317	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10073754	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs193714	0.80[CEU][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs27744	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs30384	0.85[CEU][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS 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 miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers 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 miRNA target site	178 gene(s)	inside rSNPs	diseases
7	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
9	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
10	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179286200-179310600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179286400-179287600	Enhancers	Spleen	Spleen
3	chr5:179286400-179289200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:179286400-179289400	Weak transcription	Gastric	stomach
5	chr5:179286400-179289600	Weak transcription	Small Intestine	intestine
6	chr5:179286400-179303000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:179286600-179287600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:179286600-179287600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:179286600-179287600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:179286600-179287600	Enhancers	Brain Angular Gyrus	brain
11	chr5:179286600-179287600	Enhancers	Left Ventricle	heart
12	chr5:179286600-179287600	Enhancers	Lung	lung
13	chr5:179286600-179287600	Enhancers	Pancreas	Pancrea
14	chr5:179286600-179287600	Enhancers	Psoas Muscle	Psoas
15	chr5:179286600-179287600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr5:179286600-179287800	Enhancers	Fetal Brain Male	brain
17	chr5:179286600-179287800	Enhancers	K562	blood
18	chr5:179286600-179288400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:179286600-179288400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:179286600-179288800	Weak transcription	Fetal Intestine Large	intestine
21	chr5:179286600-179289000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:179286600-179289000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:179286600-179289000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:179286600-179289000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:179286600-179289200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:179286600-179289200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:179286600-179289200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:179286600-179289200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:179286600-179289200	Weak transcription	Fetal Thymus	thymus
30	chr5:179286600-179289200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:179286600-179289200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr5:179286600-179289400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:179286600-179289400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr5:179286600-179289400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:179286600-179289400	Weak transcription	Primary T cells from cord blood	blood
36	chr5:179286600-179289400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:179286600-179289400	Weak transcription	Aorta	Aorta
38	chr5:179286600-179289400	Weak transcription	Ovary	ovary
39	chr5:179286600-179289600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:179286600-179289600	Weak transcription	Hela-S3	cervix
41	chr5:179286600-179290400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:179286600-179290800	Weak transcription	Primary B cells from cord blood	blood
43	chr5:179286600-179310600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:179286600-179310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:179286600-179311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:179286800-179287600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:179286800-179287600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:179286800-179287600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:179286800-179287600	Enhancers	Liver	Liver
50	chr5:179286800-179287600	Enhancers	Brain Cingulate Gyrus	brain

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