Variant report

Variant	rs2583406
Chromosome Location	chr4:102213720-102213721
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	chr4:102211391..102213772-chr4:102219486..102221204,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10007902	0.82[JPT][hapmap]
rs1031033	0.95[JPT][hapmap]
rs1031034	0.95[JPT][hapmap]
rs1348161	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1441433	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1530259	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1549513	0.81[JPT][hapmap]
rs1549515	0.84[JPT][hapmap]
rs1549516	0.81[JPT][hapmap]
rs1561719	0.95[EUR][1000 genomes]
rs2028475	0.94[EUR][1000 genomes]
rs2099813	0.95[EUR][1000 genomes]
rs2583389	0.95[JPT][hapmap]
rs2583392	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2583394	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2583395	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2583397	0.83[ASN][1000 genomes]
rs2583398	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2583399	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2583400	0.86[CEU][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes]
rs2583401	0.87[CEU][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes]
rs2583402	0.93[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs2583410	0.93[EUR][1000 genomes]
rs2850326	0.95[JPT][hapmap]
rs2850332	0.93[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs2850339	0.93[EUR][1000 genomes]
rs2850344	0.87[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes]
rs2850348	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850349	0.97[EUR][1000 genomes]
rs2850350	0.93[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850351	0.87[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes]
rs2850352	0.97[EUR][1000 genomes]
rs2850354	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850355	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850356	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850357	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850358	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850360	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850367	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2850369	0.87[JPT][hapmap]
rs2850370	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2850371	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2850372	0.83[ASN][1000 genomes]
rs2850954	0.94[EUR][1000 genomes]
rs2850963	0.93[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs2850967	0.93[EUR][1000 genomes]
rs2850969	0.87[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs2850974	0.85[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes]
rs2850975	0.96[EUR][1000 genomes]
rs2850976	0.93[CEU][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes]
rs4452435	0.81[JPT][hapmap]
rs755961	0.94[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs920559	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs920560	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs962384	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2583406	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102201200-102218200	Weak transcription	NHEK	skin
2	chr4:102201400-102214200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:102207000-102216600	Weak transcription	NH-A	brain
4	chr4:102207400-102214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:102207400-102214200	Weak transcription	Esophagus	oesophagus
6	chr4:102207600-102226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:102209400-102214200	Weak transcription	Aorta	Aorta
8	chr4:102209400-102214400	Weak transcription	Right Ventricle	heart
9	chr4:102209800-102214400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:102210200-102214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:102210200-102215600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr4:102210200-102225800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:102210600-102214200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:102210600-102215800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:102211000-102214200	Enhancers	Ovary	ovary
16	chr4:102211200-102215400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:102211200-102215600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:102211200-102219000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:102211400-102214200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:102211800-102214400	Weak transcription	Primary B cells from cord blood	blood
21	chr4:102212000-102214000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:102212200-102220600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:102212200-102226200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:102212400-102216600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:102212600-102213800	Weak transcription	Osteobl	bone
26	chr4:102212600-102214000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:102212600-102214200	Weak transcription	Psoas Muscle	Psoas
28	chr4:102212600-102227200	Weak transcription	Primary T cells from cord blood	blood
29	chr4:102212800-102214400	Weak transcription	Brain Anterior Caudate	brain
30	chr4:102212800-102215200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:102212800-102216800	Weak transcription	Adipose Nuclei	Adipose
32	chr4:102212800-102217400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:102212800-102221000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:102212800-102227200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:102212800-102228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:102213000-102213800	Enhancers	Fetal Heart	heart
37	chr4:102213000-102214200	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:102213000-102214200	Weak transcription	A549	lung
39	chr4:102213000-102214400	Weak transcription	Right Atrium	heart
40	chr4:102213000-102214800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:102213200-102214200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:102213200-102214400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:102213200-102218000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:102213400-102214200	Weak transcription	Pancreas	Pancrea
45	chr4:102213400-102214400	Weak transcription	Gastric	stomach
46	chr4:102213400-102221000	Weak transcription	Stomach Mucosa	stomach
47	chr4:102213600-102214200	Weak transcription	Left Ventricle	heart
48	chr4:102213600-102215000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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