Variant report

Variant	rs553253185
Chromosome Location	chr5:179233479-179233480
allele	G/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	HA-E2F1	chr5:179232882-179233648	Hela-S3	cervix:	n/a	chr5:179233079-179233088 chr5:179233382-179233391 chr5:179233029-179233044 chr5:179233379-179233389
2	POLR2A	chr5:179233032-179234049	GM12891	blood:	n/a	n/a
3	POLR2A	chr5:179232922-179234644	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:179232457-179233676	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:179232788-179233677	K562	blood:	n/a	n/a
6	MAZ	chr5:179232317-179234572	Hela-S3	cervix:	n/a	chr5:179232753-179232763 chr5:179232882-179232892 chr5:179233343-179233353
7	YY1	chr5:179232626-179233610	K562	blood:	n/a	chr5:179232825-179232834 chr5:179232879-179232893
8	POLR2A	chr5:179233376-179234601	Gliobla	brain:	n/a	n/a
9	POLR2A	chr5:179232532-179233632	GM12892	blood:	n/a	n/a
10	POLR2A	chr5:179232589-179233635	K562	blood:	n/a	n/a
11	POLR2A	chr5:179232771-179234571	GM18951	blood:	n/a	n/a
12	POLR2A	chr5:179232578-179233649	H1-neurons	neurons:	n/a	n/a
13	GABPA	chr5:179232832-179233664	MCF-7	breast:	n/a	n/a
14	POLR2A	chr5:179233053-179234095	GM10847	blood:	n/a	n/a
15	POLR2A	chr5:179232676-179233664	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr5:179224667-179233676	HL-60	blood:	n/a	n/a
17	POLR2A	chr5:179232512-179234564	MCF-7	breast:	n/a	n/a
18	TCF3	chr5:179232903-179233600	GM12878	blood:	n/a	chr5:179233243-179233257
19	POLR2A	chr5:179230590-179233696	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:179232830-179233640	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:179233088-179234566	MCF10A-Er-Src	breast:	n/a	n/a
22	MXI1	chr5:179232522-179234065	GM12878	blood:	n/a	n/a
23	CCNT2	chr5:179232488-179234597	K562	blood:	n/a	chr5:179234237-179234246
24	POLR2A	chr5:179232520-179233675	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:179230770-179234550	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:179233471-179234029	HepG2	liver:	n/a	n/a
27	POLR2A	chr5:179232911-179234557	GM19193	blood:	n/a	n/a
28	POLR2A	chr5:179232343-179234662	HUVEC	blood vessel:	n/a	n/a
29	ELF1	chr5:179232899-179233539	GM12878	blood:	n/a	chr5:179232952-179232964 chr5:179233250-179233262
30	HMGN3	chr5:179232471-179234681	K562	blood:	n/a	n/a
31	POLR2A	chr5:179232863-179234601	K562	blood:	n/a	n/a
32	MAZ	chr5:179232595-179234578	GM12878	blood:	n/a	chr5:179232753-179232763 chr5:179232882-179232892 chr5:179233343-179233353
33	TAF1	chr5:179233402-179233618	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:179233071-179234047	IMR90	lung:	n/a	n/a
35	MAZ	chr5:179232286-179233715	IMR90	lung:	n/a	chr5:179232753-179232763 chr5:179232882-179232892 chr5:179233343-179233353
36	MXI1	chr5:179233446-179233597	Hela-S3	cervix:	n/a	n/a
37	ELF1	chr5:179233266-179233570	K562	blood:	n/a	n/a
38	E2F6	chr5:179232653-179234605	K562	blood:	n/a	chr5:179233079-179233088 chr5:179232825-179232834 chr5:179233382-179233391 chr5:179234412-179234423 chr5:179233029-179233044 chr5:179233379-179233389
39	POLR2A	chr5:179232949-179234597	GM19099	blood:	n/a	n/a
40	POLR2A	chr5:179233160-179234041	GM12878	blood:	n/a	n/a
41	MXI1	chr5:179232019-179234611	IMR90	lung:	n/a	n/a
42	POLR2A	chr5:179232997-179233620	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr5:179232912-179234546	GM12878	blood:	n/a	n/a
44	YY1	chr5:179232641-179233595	HepG2	liver:	n/a	chr5:179232825-179232834 chr5:179232879-179232893
45	ZBTB7A	chr5:179232461-179234657	K562	blood:	n/a	chr5:179233377-179233384
46	ELF1	chr5:179232488-179233613	K562	blood:	n/a	chr5:179232952-179232964 chr5:179232879-179232891 chr5:179233250-179233262
47	TAF1	chr5:179233111-179233683	K562	blood:	n/a	n/a
48	POLR2A	chr5:179231839-179234641	Hela-S3	cervix:	n/a	n/a
49	YY1	chr5:179233270-179233686	GM12892	blood:	n/a	chr5:179233614-179233634
50	POLR2A	chr5:179232134-179234679	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179232651..179234632-chr5:179498072..179500275,2	MCF-7	breast:
2	chr5:179125105..179126720-chr5:179232704..179234457,2	MCF-7	breast:
3	chr5:179159604..179161312-chr5:179232221..179234868,2	MCF-7	breast:
4	chr5:179231951..179234998-chr5:179332268..179335922,5	MCF-7	breast:
5	chr5:179229039..179235504-chr5:179284286..179287391,9	MCF-7	breast:
6	chr5:179231022..179234564-chr5:179332456..179334964,4	MCF-7	breast:
7	chr5:179049195..179052432-chr5:179232038..179235083,3	K562	blood:
8	chr5:179103716..179105834-chr5:179232132..179234075,2	MCF-7	breast:
9	chr3:48487800..48488607-chr5:179233338..179233841,2	Hela-S3	cervix:
10	chr5:179123960..179129281-chr5:179231995..179235216,8	K562	blood:
11	chr5:179048743..179051829-chr5:179229515..179233744,4	MCF-7	breast:
12	chr20:52209726..52211321-chr5:179232492..179235462,2	MCF-7	breast:
13	chr5:179158130..179161320-chr5:179231546..179235366,4	K562	blood:
14	chr5:179232749..179234437-chr5:179284019..179286391,2	K562	blood:
15	chr5:179123960..179129252-chr5:179231413..179236095,7	K562	blood:
16	chr5:179232661..179233569-chr5:179247811..179248453,2	MCF-7	breast:
17	chr5:179233344..179233858-chr6:36953828..36954636,2	Hela-S3	cervix:
18	chr5:179125840..179127525-chr5:179233336..179235588,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTC4S-2	chr5:179233398-179233591	NONHSAT105629

Variant related genes	Relation type
MGAT4B	TF binding region
SQSTM1	TF binding region
ENSG00000161011	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv823361	chr5:179213324-179251243	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
10	nsv883278	chr5:179214818-179238794	Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
11	nsv883279	chr5:179214818-179248774	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
12	nsv870188	chr5:179218824-179235424	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
13	nsv883280	chr5:179220010-179238794	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
14	nsv883281	chr5:179220010-179250500	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
15	nsv883284	chr5:179220638-179246415	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	158 gene(s)	inside rSNPs	diseases
16	nsv883285	chr5:179223023-179238794	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	153 gene(s)	inside rSNPs	diseases
17	nsv600668	chr5:179227865-179242581	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	esv3403342	chr5:179231746-179236044	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	esv3427312	chr5:179232371-179234919	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	esv3325781	chr5:179232971-179235519	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	esv988291	chr5:179233076-179240737	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179232000-179234800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr5:179232000-179235200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:179232200-179234600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:179232200-179234600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:179232200-179234600	Active TSS	NHEK	skin
6	chr5:179232200-179234800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:179232200-179234800	Active TSS	Colon Smooth Muscle	Colon
8	chr5:179232400-179233600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:179232400-179234400	Active TSS	Aorta	Aorta
10	chr5:179232400-179234600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:179232400-179234600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:179232400-179234600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr5:179232400-179234600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr5:179232400-179234600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:179232400-179234600	Active TSS	Brain Substantia Nigra	brain
16	chr5:179232400-179234600	Active TSS	Fetal Kidney	kidney
17	chr5:179232400-179234600	Active TSS	HSMMtube	muscle
18	chr5:179232400-179234600	Active TSS	NHDF-Ad	bronchial
19	chr5:179232400-179234600	Active TSS	NHLF	lung
20	chr5:179232400-179234800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:179232400-179234800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:179232400-179235000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr5:179232400-179235000	Active TSS	A549	lung
24	chr5:179232400-179235200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr5:179232600-179233800	Active TSS	Right Atrium	heart
26	chr5:179232600-179234400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:179232600-179234400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:179232600-179234600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:179232600-179234600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:179232600-179234600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:179232600-179234600	Active TSS	Liver	Liver
32	chr5:179232600-179234600	Active TSS	Brain Anterior Caudate	brain
33	chr5:179232600-179234600	Active TSS	Brain Cingulate Gyrus	brain
34	chr5:179232600-179234600	Active TSS	Brain Hippocampus Middle	brain
35	chr5:179232600-179234600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr5:179232600-179234600	Active TSS	Esophagus	oesophagus
37	chr5:179232600-179234600	Active TSS	Fetal Lung	lung
38	chr5:179232600-179234600	Active TSS	Ovary	ovary
39	chr5:179232600-179234600	Active TSS	Right Ventricle	heart
40	chr5:179232600-179234600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr5:179232600-179234600	Active TSS	Small Intestine	intestine
42	chr5:179232600-179234600	Active TSS	GM12878-XiMat	blood
43	chr5:179232600-179234600	Active TSS	NH-A	brain
44	chr5:179232600-179234800	Active TSS	Brain Angular Gyrus	brain
45	chr5:179232600-179234800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:179232600-179234800	Active TSS	Psoas Muscle	Psoas
47	chr5:179232600-179234800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr5:179232600-179234800	Active TSS	Hela-S3	cervix
49	chr5:179232600-179234800	Active TSS	Osteobl	bone
50	chr5:179232600-179235000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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