Variant report

Variant	rs12656758
Chromosome Location	chr5:179518590-179518591
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	CTCF	chr5:179518500-179518650	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr5:179518092-179518647	A549	lung:	n/a	n/a
3	MAX	chr5:179517924-179518659	MCF-7	breast:	n/a	chr5:179518154-179518165 chr5:179518155-179518164 chr5:179518155-179518164 chr5:179518146-179518162 chr5:179518154-179518164 chr5:179518154-179518165 chr5:179518156-179518163
4	KAP1	chr5:179518149-179518636	U2OS	brain:	n/a	n/a
5	MAX	chr5:179517927-179518702	A549	lung:	n/a	chr5:179518154-179518165 chr5:179518155-179518164 chr5:179518155-179518164 chr5:179518146-179518162 chr5:179518154-179518164 chr5:179518154-179518165 chr5:179518156-179518163
6	E2F6	chr5:179517954-179518741	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr5:179518034-179518687	MCF-7	breast:	n/a	n/a
8	CTCF	chr5:179517273-179518684	HCT-116	colon:	n/a	chr5:179517625-179517638 chr5:179517623-179517641 chr5:179517625-179517638 chr5:179517629-179517638 chr5:179517626-179517636 chr5:179517624-179517640 chr5:179517618-179517639
9	POLR2A	chr5:179518577-179518628	H1-hESC	embryonic stem cell:	n/a	n/a
10	STAT3	chr5:179518452-179518633	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr5:179518155-179518670	MCF-7	breast:	n/a	n/a
12	RAD21	chr5:179518022-179518603	MCF-7	breast:	n/a	n/a
13	CTCF	chr5:179518083-179518601	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr5:179517943-179518663	HCT-116	colon:	n/a	n/a
15	MAX	chr5:179517951-179518639	H1-hESC	embryonic stem cell:	n/a	chr5:179518154-179518165 chr5:179518155-179518164 chr5:179518155-179518164 chr5:179518146-179518162 chr5:179518154-179518164 chr5:179518154-179518165 chr5:179518156-179518163
16	RAD21	chr5:179518087-179518636	MCF-7	breast:	n/a	n/a
17	RAD21	chr5:179518198-179518606	A549	lung:	n/a	n/a
18	RAD21	chr5:179517931-179518688	HCT-116	colon:	n/a	n/a
19	RAD21	chr5:179518188-179518591	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr5:179516894-179518790	A549	lung:	n/a	chr5:179517625-179517638 chr5:179517623-179517641 chr5:179517625-179517638 chr5:179517629-179517638 chr5:179517626-179517636 chr5:179517624-179517640 chr5:179517618-179517639
21	MAX	chr5:179517942-179518644	A549	lung:	n/a	chr5:179518154-179518165 chr5:179518155-179518164 chr5:179518155-179518164 chr5:179518146-179518162 chr5:179518154-179518164 chr5:179518154-179518165 chr5:179518156-179518163

No.	Distal block	Cell Line	Cell type
1	chr5:179451009..179454455-chr5:179516109..179519066,3	MCF-7	breast:
2	chr5:179448640..179449492-chr5:179517155..179518787,5	MCF-7	breast:
3	chr5:179388366..179391138-chr5:179517585..179519806,2	K562	blood:
4	chr5:179104426..179106670-chr5:179516761..179519080,2	MCF-7	breast:
5	chr5:179492115..179494311-chr5:179517115..179518627,2	MCF-7	breast:
6	chr5:179495694..179500359-chr5:179515816..179519621,6	MCF-7	breast:
7	chr5:179517772..179520759-chr5:179536622..179539248,2	MCF-7	breast:
8	chr5:179518292..179520917-chr5:179894256..179896399,2	MCF-7	breast:
9	chr5:179497628..179501303-chr5:179515558..179519468,8	MCF-7	breast:
10	chr5:179505842..179508438-chr5:179517931..179520878,2	K562	blood:
11	chr5:179448515..179449607-chr5:179517585..179518817,9	MCF-7	breast:
12	chr5:179517603..179519826-chr5:179526905..179528736,2	K562	blood:
13	chr5:179447316..179449244-chr5:179516942..179519007,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253480	TF binding region
ENSG00000127022	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000249412	Chromatin interaction
ENSG00000225051	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12656459	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179513200-179520800	Weak transcription	Spleen	Spleen
2	chr5:179517600-179518600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:179517600-179518600	Enhancers	Primary B cells from cord blood	blood
4	chr5:179517600-179518600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:179517600-179518600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:179517600-179518600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:179517600-179518600	Enhancers	Brain Hippocampus Middle	brain
8	chr5:179517600-179518600	Enhancers	Fetal Thymus	thymus
9	chr5:179517600-179518600	Enhancers	Stomach Mucosa	stomach
10	chr5:179517600-179519400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:179517600-179521200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:179517600-179521400	Enhancers	Primary hematopoietic stem cells	blood
13	chr5:179517800-179518600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:179517800-179518600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:179517800-179518600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:179517800-179518600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr5:179517800-179518600	Enhancers	Primary B cells from peripheral blood	blood
18	chr5:179517800-179518600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr5:179517800-179518600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr5:179517800-179518600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:179517800-179518600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr5:179517800-179518600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:179517800-179518600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:179517800-179518600	Enhancers	Colon Smooth Muscle	Colon
25	chr5:179517800-179518600	Enhancers	Fetal Muscle Trunk	muscle
26	chr5:179517800-179518600	Enhancers	Pancreas	Pancrea
27	chr5:179517800-179518600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:179517800-179518800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:179517800-179518800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr5:179517800-179519400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:179517800-179520600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr5:179517800-179520800	Enhancers	K562	blood
33	chr5:179518000-179518600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:179518000-179518600	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr5:179518200-179518600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr5:179518200-179518600	Enhancers	Primary T cells from cord blood	blood
37	chr5:179518200-179518600	Flanking Active TSS	Liver	Liver
38	chr5:179518200-179519000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:179518200-179519400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:179518200-179520800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:179518400-179518600	Enhancers	H9 Cell Line	embryonic stem cell
42	chr5:179518400-179518600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr5:179518400-179518600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:179518400-179518600	Enhancers	Esophagus	oesophagus
45	chr5:179518400-179518600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr5:179518400-179518600	Enhancers	Stomach Smooth Muscle	stomach
47	chr5:179518400-179518600	Enhancers	A549	lung
48	chr5:179518400-179518800	Enhancers	Duodenum Mucosa	Duodenum
49	chr5:179518400-179518800	Enhancers	Fetal Kidney	kidney
50	chr5:179518400-179519200	Weak transcription	H1 Cell Line	embryonic stem cell

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