Variant report

Variant	rs1603886
Chromosome Location	chr4:129450677-129450678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129444037..129452105-chr4:129473073..129478954,15	MCF-7	breast:
2	chr4:129305678..129308286-chr4:129449274..129450923,2	MCF-7	breast:
3	chr4:129449656..129451210-chr4:129491990..129494350,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273077	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10518533	0.86[ASN][1000 genomes]
rs11733387	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11937124	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13115644	0.82[EUR][1000 genomes]
rs1603887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17337491	1.00[ASW][hapmap]
rs2062456	1.00[ASW][hapmap];0.83[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs2133465	1.00[ASW][hapmap]
rs4305531	1.00[ASW][hapmap]
rs4362840	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4975185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975186	0.87[ASN][1000 genomes]
rs6534679	1.00[ASW][hapmap]
rs6534686	0.96[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6534687	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6534691	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821679	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6840580	1.00[ASW][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs6849290	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7441245	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1017672	chr4:129450450-129603977	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr4:129444800-129451000	Enhancers	HSMM	muscle
2	chr4:129444800-129451000	Enhancers	Osteobl	bone
3	chr4:129445000-129451000	Enhancers	NHDF-Ad	bronchial
4	chr4:129445200-129451000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:129447400-129450800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:129447400-129450800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr4:129447400-129451000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:129448000-129456400	Weak transcription	Stomach Mucosa	stomach
9	chr4:129448400-129451000	Enhancers	HSMMtube	muscle
10	chr4:129448600-129451000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:129448600-129451000	Enhancers	Fetal Heart	heart
12	chr4:129448600-129451000	Enhancers	NH-A	brain
13	chr4:129448800-129451000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:129449000-129450800	Enhancers	Fetal Muscle Leg	muscle
15	chr4:129449000-129451000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:129449000-129451000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:129449000-129451000	Enhancers	NHLF	lung
18	chr4:129449200-129450800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:129449200-129451000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:129449200-129451000	Flanking Active TSS	A549	lung
21	chr4:129449200-129451000	Enhancers	HUVEC	blood vessel
22	chr4:129449400-129450800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:129449400-129450800	Enhancers	Stomach Smooth Muscle	stomach
24	chr4:129449400-129451000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr4:129449400-129451000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:129449400-129451000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:129449400-129451000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:129449400-129451000	Enhancers	HMEC	breast
29	chr4:129449600-129450800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:129449600-129450800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:129449600-129450800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr4:129449600-129451000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:129449600-129451000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:129449600-129451000	Enhancers	Hela-S3	cervix
35	chr4:129449800-129451000	Enhancers	Adipose Nuclei	Adipose
36	chr4:129449800-129451000	Enhancers	Placenta	Placenta
37	chr4:129450000-129450800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr4:129450000-129450800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:129450000-129450800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr4:129450000-129450800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:129450000-129450800	Enhancers	Ovary	ovary
42	chr4:129450000-129450800	Enhancers	Rectal Smooth Muscle	rectum
43	chr4:129450000-129450800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr4:129450200-129450800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr4:129450400-129451000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr4:129450600-129450800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:129450600-129451000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:129450600-129451000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:129450600-129451000	Enhancers	Psoas Muscle	Psoas
50	chr4:129450600-129451000	Enhancers	NHEK	skin

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