Variant report

Variant	rs3845417
Chromosome Location	chr1:180896902-180896903
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	POLR2A	chr1:180896478-180896964	H1-neurons	neurons:	n/a	n/a
2	EP300	chr1:180894092-180899177	SK-N-SH	brain:	n/a	chr1:180896188-180896202
3	REST	chr1:180896852-180897252	PFSK-1	brain:	n/a	chr1:180897057-180897066
4	REST	chr1:180896849-180897223	SK-N-SH	brain:	n/a	chr1:180897057-180897066
5	REST	chr1:180896890-180897161	PANC-1	pancreas:	n/a	chr1:180897057-180897066
6	REST	chr1:180896826-180897317	ECC-1	luminal epithelium:	n/a	chr1:180897057-180897066
7	REST	chr1:180896804-180897242	PFSK-1	brain:	n/a	chr1:180897057-180897066

No.	Distal block	Cell Line	Cell type
1	chr1:180894020..180896970-chr1:180921543..180923993,2	MCF-7	breast:
2	chr1:180895591..180897824-chr1:181056738..181059275,3	MCF-7	breast:
3	chr1:180891831..180893938-chr1:180895346..180897268,3	K562	blood:

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

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11810413	1.00[MEX][hapmap]
rs58172825	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:90 , 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	chr1:180890400-180898200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:180890600-180898000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:180890800-180898200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:180890800-180898600	Enhancers	Placenta	Placenta
9	chr1:180891000-180897800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:180891600-180901000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:180891800-180898200	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:180893000-180897400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:180893000-180897400	Weak transcription	Lung	lung
14	chr1:180893000-180897800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:180893000-180898000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:180893600-180897800	Enhancers	Fetal Muscle Leg	muscle
17	chr1:180894000-180897800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:180894200-180897000	Flanking Active TSS	HepG2	liver
19	chr1:180894200-180897200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:180894200-180897400	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:180894200-180897800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:180894200-180898000	Enhancers	Fetal Heart	heart
23	chr1:180894200-180898000	Enhancers	Fetal Lung	lung
24	chr1:180894200-180898000	Enhancers	Fetal Stomach	stomach
25	chr1:180894200-180898200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:180894200-180898600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:180894200-180899000	Enhancers	Left Ventricle	heart
28	chr1:180894400-180899000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:180894600-180897000	Enhancers	Fetal Intestine Large	intestine
30	chr1:180894600-180897400	Enhancers	HSMM	muscle
31	chr1:180894600-180898200	Enhancers	Colon Smooth Muscle	Colon
32	chr1:180894600-180898200	Enhancers	Right Ventricle	heart
33	chr1:180894600-180899200	Enhancers	Ovary	ovary
34	chr1:180895200-180897200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:180895200-180897800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:180895200-180897800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:180895200-180902200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:180895400-180897000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:180895400-180900800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:180895400-180914200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:180895600-180898200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:180895600-180899400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:180895800-180897800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:180896000-180898000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:180896000-180898000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:180896000-180898200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:180896000-180902600	Enhancers	Thymus	Thymus
48	chr1:180896200-180897400	Weak transcription	Psoas Muscle	Psoas
49	chr1:180896200-180897800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:180896200-180897800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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