Variant report

Variant	rs58172825
Chromosome Location	chr1:180895344-180895345
allele	A/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	TAF1	chr1:180895258-180896187	H1-neurons	neurons:	n/a	n/a
2	REST	chr1:180895315-180896250	H1-neurons	neurons:	n/a	n/a
3	EP300	chr1:180894092-180899177	SK-N-SH	brain:	n/a	chr1:180896188-180896202
4	ESR1	chr1:180895253-180895625	ECC-1	luminal epithelium:	n/a	chr1:180895448-180895465
5	REST	chr1:180895055-180896618	H1-neurons	neurons:	n/a	chr1:180896323-180896337 chr1:180896327-180896340 chr1:180896323-180896343 chr1:180896323-180896343
6	ZNF263	chr1:180894869-180896749	K562	blood:	n/a	n/a
7	POLR2A	chr1:180895261-180896458	H1-neurons	neurons:	n/a	n/a
8	GATA2	chr1:180894667-180896194	SH-SY5Y	brain:	n/a	n/a
9	POLR2A	chr1:180895285-180896202	H1-neurons	neurons:	n/a	n/a
10	TCF12	chr1:180895271-180896273	SK-N-SH	brain:	n/a	chr1:180896135-180896145

No.	Distal block	Cell Line	Cell type
1	chr1:180894020..180896970-chr1:180921543..180923993,2	MCF-7	breast:
2	chr1:180892738..180895948-chr1:181056431..181059504,3	K562	blood:
3	chr1:180888347..180891443-chr1:180893391..180896382,5	K562	blood:
4	chr1:180879805..180882226-chr1:180894957..180896873,2	MCF-7	breast:
5	chr1:180893588..180895646-chr1:181053051..181055501,3	MCF-7	breast:
6	chr1:180865980..180867777-chr1:180893565..180896342,2	K562	blood:

Variant related genes	Relation type
KIAA1614	TF binding region
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs3845417	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1001918	chr1:180886750-180908005	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180886000-180911000	Enhancers	Fetal Thymus	thymus
2	chr1:180887600-180915800	Weak transcription	Osteobl	bone
3	chr1:180888400-180897600	Weak transcription	Aorta	Aorta
4	chr1:180888600-180917200	Weak transcription	Gastric	stomach
5	chr1:180890400-180895600	Enhancers	Thymus	Thymus
6	chr1:180890400-180898200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:180890600-180898000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:180890800-180898200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:180890800-180898600	Enhancers	Placenta	Placenta
10	chr1:180891000-180897800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:180891400-180896600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:180891600-180901000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:180891800-180898200	Enhancers	Fetal Muscle Trunk	muscle
14	chr1:180892400-180895400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:180892600-180895400	Enhancers	Brain Anterior Caudate	brain
16	chr1:180893000-180895600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:180893000-180896600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:180893000-180897400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:180893000-180897400	Weak transcription	Lung	lung
20	chr1:180893000-180897800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:180893000-180898000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:180893200-180895400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:180893200-180896800	Enhancers	K562	blood
24	chr1:180893600-180895600	Weak transcription	NHEK	skin
25	chr1:180893600-180897800	Enhancers	Fetal Muscle Leg	muscle
26	chr1:180894000-180895600	Weak transcription	NH-A	brain
27	chr1:180894000-180897800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:180894200-180895400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:180894200-180895400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:180894200-180895400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr1:180894200-180895400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:180894200-180895400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:180894200-180895400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:180894200-180895600	Enhancers	Brain Germinal Matrix	brain
35	chr1:180894200-180895800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:180894200-180896400	Enhancers	Spleen	Spleen
37	chr1:180894200-180896600	Enhancers	Fetal Brain Male	brain
38	chr1:180894200-180897000	Flanking Active TSS	HepG2	liver
39	chr1:180894200-180897200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:180894200-180897400	Enhancers	Primary hematopoietic stem cells	blood
41	chr1:180894200-180897800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:180894200-180898000	Enhancers	Fetal Heart	heart
43	chr1:180894200-180898000	Enhancers	Fetal Lung	lung
44	chr1:180894200-180898000	Enhancers	Fetal Stomach	stomach
45	chr1:180894200-180898200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:180894200-180898600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:180894200-180899000	Enhancers	Left Ventricle	heart
48	chr1:180894400-180895600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:180894400-180896400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:180894400-180896400	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links