Variant report

Variant	rs154003
Chromosome Location	chr5:127678992-127678993
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	chr5:127673442..127675175-chr5:127677395..127679627,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138829	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10519991	1.00[CHB][hapmap]
rs154000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154001	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs154002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17608902	1.00[CHB][hapmap]
rs17676837	1.00[CHB][hapmap]
rs17676891	0.85[CHB][hapmap]
rs255725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs255727	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs255730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27859	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27913	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs364671	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805639	1.00[ASN][1000 genomes]
rs39938	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs422728	0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs468026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs468229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs469294	0.93[CEU][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][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	nsv599697	chr5:127563563-127731210	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv830483	chr5:127595570-127705124	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127638200-127685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:127657400-127685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:127658000-127683600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:127659200-127693600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:127659200-127693800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:127660600-127683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:127660600-127687000	Weak transcription	Fetal Brain Female	brain
8	chr5:127661200-127683800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:127661200-127693000	Weak transcription	NHLF	lung
10	chr5:127661200-127693600	Strong transcription	Placenta	Placenta
11	chr5:127661800-127683600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:127662000-127681400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:127664600-127682000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:127668800-127681200	Weak transcription	Gastric	stomach
15	chr5:127671800-127681000	Weak transcription	Ovary	ovary
16	chr5:127672000-127746000	Weak transcription	NHDF-Ad	bronchial
17	chr5:127673200-127679800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:127673200-127683800	Strong transcription	Fetal Stomach	stomach
19	chr5:127673400-127680000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:127673400-127681200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:127673800-127706400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:127674000-127680800	Weak transcription	HUVEC	blood vessel
23	chr5:127674800-127684600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:127675600-127679600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:127675600-127681200	Weak transcription	Right Atrium	heart
26	chr5:127675600-127742200	Weak transcription	Fetal Intestine Small	intestine
27	chr5:127676600-127681400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr5:127676600-127681600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:127676600-127681800	Strong transcription	Fetal Muscle Leg	muscle
30	chr5:127676600-127686800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:127676800-127681600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr5:127676800-127683800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:127677000-127679200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:127677000-127681600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:127677200-127679000	Strong transcription	Fetal Kidney	kidney
36	chr5:127677200-127681600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:127677400-127681600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:127677600-127694800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:127677800-127711400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:127678000-127679200	Strong transcription	Fetal Intestine Large	intestine
41	chr5:127678000-127679800	Strong transcription	Fetal Heart	heart
42	chr5:127678000-127681200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:127678000-127681600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:127678200-127679200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:127678200-127679200	Strong transcription	Fetal Lung	lung
46	chr5:127678200-127681200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:127678200-127686200	Weak transcription	NH-A	brain
48	chr5:127678400-127680000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr5:127678600-127679200	Strong transcription	A549	lung
50	chr5:127678600-127679600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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