Variant report

Variant	rs3819951
Chromosome Location	chr1:180600220-180600221
allele	A/C/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	EP300	chr1:180600162-180600565	GM12878	blood:	n/a	n/a
2	PAX5	chr1:180600058-180600284	GM12878	blood:	n/a	n/a
3	PAX5	chr1:180599992-180600507	GM12878	blood:	n/a	n/a
4	ZNF384	chr1:180600109-180600969	GM12878	blood:	n/a	n/a
5	EBF1	chr1:180600178-180600653	GM12878	blood:	n/a	chr1:180600444-180600454 chr1:180600443-180600456 chr1:180600443-180600454 chr1:180600445-180600454 chr1:180600445-180600454
6	EBF1	chr1:180600206-180600664	GM12878	blood:	n/a	chr1:180600444-180600454 chr1:180600443-180600456 chr1:180600443-180600454 chr1:180600445-180600454 chr1:180600445-180600454
7	EBF1	chr1:180600187-180601344	GM12878	blood:	n/a	chr1:180600444-180600454 chr1:180600443-180600456 chr1:180600443-180600454 chr1:180600445-180600454 chr1:180600445-180600454
8	CHD2	chr1:180600208-180601930	GM12878	blood:	n/a	chr1:180601649-180601656

No.	Distal block	Cell Line	Cell type
1	chr1:180486117..180489431-chr1:180599413..180603700,5	MCF-7	breast:
2	chr1:180489178..180492158-chr1:180598991..180600573,2	K562	blood:
3	chr1:180599642..180602569-chr1:180990925..180993189,3	MCF-7	breast:
4	chr1:180599613..180601233-chr1:180805149..180807716,2	K562	blood:
5	chr1:180470531..180473320-chr1:180599332..180602016,2	K562	blood:
6	chr1:180470493..180473506-chr1:180597830..180602116,4	MCF-7	breast:
7	chr1:180598794..180600928-chr1:181056427..181059135,2	K562	blood:

Variant related genes	Relation type
XPR1	TF binding region
ENSG00000135847	Chromatin interaction
ENSG00000135823	Chromatin interaction
ENSG00000143324	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000206905	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12118646	0.91[ASN][1000 genomes]
rs3753202	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819953	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3845406	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4083591	0.82[AFR][1000 genomes]
rs4651073	0.92[ASN][1000 genomes]
rs6661105	0.80[ASN][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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180581800-180600600	Weak transcription	Fetal Heart	heart
2	chr1:180593200-180601000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:180598000-180600400	Weak transcription	Spleen	Spleen
4	chr1:180599000-180600800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:180599200-180600800	Enhancers	Adipose Nuclei	Adipose
6	chr1:180599400-180600400	Enhancers	Duodenum Mucosa	Duodenum
7	chr1:180599400-180600600	Enhancers	Left Ventricle	heart
8	chr1:180599400-180600800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180599400-180600800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:180599400-180600800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:180599400-180601000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:180599400-180601000	Enhancers	Osteobl	bone
13	chr1:180599600-180600400	Enhancers	Dnd41	blood
14	chr1:180599600-180600600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr1:180599600-180601000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:180599600-180601200	Weak transcription	Right Atrium	heart
17	chr1:180599600-180601200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:180599800-180600600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:180599800-180600600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:180599800-180601000	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:180600000-180600600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr1:180600000-180600600	Enhancers	GM12878-XiMat	blood
23	chr1:180600000-180600800	Enhancers	Right Ventricle	heart
24	chr1:180600000-180601000	Enhancers	Fetal Intestine Large	intestine
25	chr1:180600000-180601200	Enhancers	Primary B cells from cord blood	blood
26	chr1:180600200-180600400	Active TSS	Stomach Smooth Muscle	stomach
27	chr1:180600200-180600600	Active TSS	Brain Substantia Nigra	brain
28	chr1:180600200-180600600	Enhancers	Fetal Thymus	thymus
29	chr1:180600200-180600800	Enhancers	Fetal Kidney	kidney
30	chr1:180600200-180600800	Enhancers	Psoas Muscle	Psoas
31	chr1:180600200-180600800	Flanking Active TSS	HepG2	liver
32	chr1:180600200-180600800	Enhancers	K562	blood
33	chr1:180600200-180601000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:180600200-180601000	Enhancers	Stomach Mucosa	stomach
35	chr1:180600200-180601200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:180600200-180601200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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