Variant report

Variant	rs2874800
Chromosome Location	chr4:20260038-20260039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:20252097..20254985-chr4:20256141..20260392,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145147	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13143450	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1323068	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196476	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2208946	0.81[EUR][1000 genomes]
rs2322459	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2322460	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4697156	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447951	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447952	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7692329	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878736	chr4:20233035-20279858	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv878737	chr4:20233035-20282334	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv878738	chr4:20255306-20300192	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv878739	chr4:20255306-20307922	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20257600-20266200	Weak transcription	HMEC	breast
2	chr4:20257600-20268200	Weak transcription	Brain Angular Gyrus	brain
3	chr4:20257800-20268400	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:20258000-20264400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:20258000-20275400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:20258200-20260400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
7	chr4:20258200-20261200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:20258200-20299400	Weak transcription	Fetal Stomach	stomach
9	chr4:20258400-20266200	Weak transcription	NHEK	skin
10	chr4:20258400-20274000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:20259000-20269600	Weak transcription	HUVEC	blood vessel
12	chr4:20259200-20260400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:20259200-20261000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:20259200-20261600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:20259200-20267600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:20259400-20261200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:20259400-20266000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:20259800-20261400	Weak transcription	NHLF	lung
19	chr4:20259800-20262600	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:20260000-20261000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:20260000-20261000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:20260000-20261000	Weak transcription	Osteobl	bone
23	chr4:20260000-20261200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:20260000-20261200	Weak transcription	Fetal Lung	lung
25	chr4:20260000-20261400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:20260000-20262400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:20260000-20265800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:20260000-20273600	Weak transcription	Fetal Kidney	kidney
29	chr4:20260000-20273800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:20260000-20276200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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