Variant report

Variant	rs56981472
Chromosome Location	chr1:228133609-228133610
allele	A/C
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	SMC3	chr1:228133302-228134695	Hela-S3	cervix:	n/a	chr1:228134476-228134490
2	NFIC	chr1:228132802-228134590	ECC-1	luminal epithelium:	n/a	n/a
3	RAD21	chr1:228133527-228134948	HCT-116	colon:	n/a	chr1:228134540-228134553 chr1:228133662-228133672 chr1:228134542-228134554 chr1:228134247-228134260 chr1:228134472-228134491 chr1:228134244-228134263 chr1:228134249-228134261
4	SMARCC1	chr1:228133155-228135003	Hela-S3	cervix:	n/a	chr1:228134128-228134137 chr1:228134129-228134138
5	EP300	chr1:228132871-228133698	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr1:228133604-228134831	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr1:228133609-228134987	A549	lung:	n/a	chr1:228134476-228134489 chr1:228134246-228134259 chr1:228134408-228134416 chr1:228134536-228134554 chr1:228134474-228134492 chr1:228134539-228134552
8	TEAD4	chr1:228133419-228134821	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:
2	chr1:228128193..228132003-chr1:228132864..228136285,5	K562	blood:
3	chr1:227668674..227670909-chr1:228132996..228135625,2	K562	blood:
4	chr1:228129106..228132233-chr1:228133265..228135585,4	MCF-7	breast:
5	chr1:227727960..227729815-chr1:228131832..228133962,2	MCF-7	breast:
6	chr1:227922958..227924817-chr1:228133058..228135872,2	MCF-7	breast:

Variant related genes	Relation type
MIR5008	TF binding region
ENSG00000143740	Chromatin interaction
ENSG00000264483	Chromatin interaction
ENSG00000237193	Chromatin interaction
ENSG00000081692	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs55694280	0.90[AFR][1000 genomes]
rs56280452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58696607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60751757	0.90[AFR][1000 genomes]
rs74140819	0.91[AFR][1000 genomes]
rs74140821	1.00[AFR][1000 genomes]
rs74140822	1.00[AFR][1000 genomes]
rs74140823	1.00[AFR][1000 genomes]
rs8192631	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
9	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228109800-228134000	Weak transcription	Right Atrium	heart
3	chr1:228126200-228134400	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:228129400-228134400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr1:228130600-228134400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:228130800-228133800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:228131800-228133800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:228131800-228133800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:228131800-228134000	Enhancers	Fetal Lung	lung
10	chr1:228131800-228134200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:228132000-228133800	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:228132000-228134200	Enhancers	Right Ventricle	heart
13	chr1:228132000-228134400	Enhancers	Left Ventricle	heart
14	chr1:228132200-228133800	Enhancers	Esophagus	oesophagus
15	chr1:228132200-228133800	Enhancers	Pancreas	Pancrea
16	chr1:228132200-228134000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:228132200-228134000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:228132200-228134200	Enhancers	Spleen	Spleen
19	chr1:228132200-228134400	Flanking Active TSS	Rectal Smooth Muscle	rectum
20	chr1:228132400-228134000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:228132600-228133800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:228132600-228134000	Enhancers	Gastric	stomach
23	chr1:228132600-228134000	Flanking Active TSS	Psoas Muscle	Psoas
24	chr1:228132800-228133800	Enhancers	Fetal Intestine Large	intestine
25	chr1:228132800-228134000	Flanking Active TSS	Hela-S3	cervix
26	chr1:228132800-228134400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr1:228132800-228134600	Enhancers	Stomach Mucosa	stomach
28	chr1:228133000-228133800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
29	chr1:228133000-228133800	Enhancers	Ovary	ovary
30	chr1:228133000-228134000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:228133000-228134200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:228133000-228134200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr1:228133000-228134400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:228133000-228134600	Enhancers	Lung	lung
35	chr1:228133000-228134800	Bivalent Enhancer	Placenta	Placenta
36	chr1:228133000-228135000	Flanking Active TSS	HMEC	breast
37	chr1:228133200-228133800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:228133200-228133800	Enhancers	Brain Substantia Nigra	brain
39	chr1:228133200-228134000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:228133200-228134000	Enhancers	Primary hematopoietic stem cells	blood
41	chr1:228133200-228134200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:228133200-228134200	Flanking Active TSS	HSMM	muscle
43	chr1:228133200-228134200	Flanking Active TSS	HSMMtube	muscle
44	chr1:228133400-228133800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:228133400-228133800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:228133400-228133800	Enhancers	Brain Hippocampus Middle	brain
47	chr1:228133400-228134000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:228133400-228134000	Enhancers	A549	lung
49	chr1:228133400-228134400	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr1:228133400-228134400	Flanking Active TSS	Fetal Heart	heart

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