Variant report

Variant	rs41080
Chromosome Location	chr5:127623697-127623698
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127611003..127612577-chr5:127622230..127624311,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12656510	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs32207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32213	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39939	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs42280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469913	0.83[EUR][1000 genomes]
rs6862992	0.92[AFR][1000 genomes]
rs6884264	0.92[AFR][1000 genomes]
rs72663358	0.83[EUR][1000 genomes]
rs72663359	0.81[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	nsv830482	chr5:127475398-127665377	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127589000-127670200	Weak transcription	NHDF-Ad	bronchial
2	chr5:127592800-127624400	Weak transcription	A549	lung
3	chr5:127592800-127631600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:127593800-127635200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:127596200-127623800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:127598800-127623800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:127599400-127624200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:127599400-127624200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:127600800-127624200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:127605200-127628800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr5:127608000-127629600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:127612800-127662400	Weak transcription	HUVEC	blood vessel
13	chr5:127614400-127635200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:127614600-127644800	Weak transcription	Ovary	ovary
15	chr5:127614600-127661000	Weak transcription	Fetal Kidney	kidney
16	chr5:127616000-127624000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:127618000-127629400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:127618400-127629600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:127619400-127629400	Strong transcription	Placenta	Placenta
20	chr5:127620200-127626400	Strong transcription	Fetal Muscle Leg	muscle
21	chr5:127620200-127639600	Weak transcription	Osteobl	bone
22	chr5:127621200-127628600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:127621600-127625400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:127621600-127625800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:127621600-127626200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:127621600-127626600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:127621800-127627400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:127621800-127628600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:127622000-127628600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:127622000-127628800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:127622200-127624600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:127622200-127624600	Strong transcription	Left Ventricle	heart
33	chr5:127622200-127625000	Strong transcription	Fetal Lung	lung
34	chr5:127622200-127625800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:127622200-127627800	Strong transcription	HMEC	breast
36	chr5:127622400-127626400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:127622400-127626400	Strong transcription	NHEK	skin
38	chr5:127622400-127629000	Strong transcription	Fetal Stomach	stomach
39	chr5:127622600-127625000	Strong transcription	Fetal Intestine Large	intestine
40	chr5:127622800-127625000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:127622800-127628600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:127622800-127662000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:127623000-127625000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:127623200-127625800	Weak transcription	NH-A	brain
45	chr5:127623400-127623800	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr5:127623400-127625000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:127623400-127625200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:127623600-127623800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:127623600-127624800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:127623600-127628800	Strong transcription	Fetal Heart	heart

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