Variant report

Variant	rs1438554
Chromosome Location	chr3:105072488-105072489
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	chr3:105072055..105074262-chr3:105075883..105078714,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12497260	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13065937	0.92[CHB][hapmap]
rs13070790	0.95[CHB][hapmap]
rs13075944	0.87[CHB][hapmap]
rs13079517	0.91[CHB][hapmap]
rs13085657	0.91[CHB][hapmap]
rs13092913	0.91[CHB][hapmap]
rs13095216	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13095274	0.97[ASN][1000 genomes]
rs1438544	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1438546	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438549	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs1438551	0.92[CHB][hapmap]
rs1438553	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16851175	0.91[CHB][hapmap]
rs2399046	0.95[CHB][hapmap]
rs4589964	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4894926	0.92[CHB][hapmap]
rs55934921	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62262153	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6437579	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6437582	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6437583	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6437584	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6773531	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6793758	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6797065	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6797259	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6804633	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7611398	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7620029	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7620713	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7626665	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7634168	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7635959	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9288801	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs976530	0.91[CHB][hapmap]
rs9852729	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869867	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9880342	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9883403	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105068600-105074600	Enhancers	HMEC	breast
2	chr3:105071000-105078200	Weak transcription	A549	lung
3	chr3:105071400-105073200	Weak transcription	NHDF-Ad	bronchial
4	chr3:105071400-105073400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:105071600-105072800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:105071800-105074600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:105072200-105072600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr3:105072200-105072600	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr3:105072200-105072800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:105072200-105073200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:105072200-105073200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:105072200-105073200	Active TSS	Brain Hippocampus Middle	brain
13	chr3:105072200-105073400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:105072200-105073600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:105072200-105073600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:105072200-105073600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:105072200-105073800	Flanking Active TSS	HUVEC	blood vessel
18	chr3:105072400-105072600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:105072400-105072600	Bivalent Enhancer	Primary B cells from cord blood	blood
20	chr3:105072400-105072600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:105072400-105072600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
22	chr3:105072400-105072600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:105072400-105072600	Bivalent Enhancer	Adipose Nuclei	Adipose
24	chr3:105072400-105072600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
25	chr3:105072400-105072600	Active TSS	Esophagus	oesophagus
26	chr3:105072400-105072600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr3:105072400-105072600	Active TSS	Fetal Stomach	stomach
28	chr3:105072400-105072600	Enhancers	Left Ventricle	heart
29	chr3:105072400-105072600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
30	chr3:105072400-105072600	Bivalent/Poised TSS	Right Atrium	heart
31	chr3:105072400-105072600	Flanking Active TSS	Right Ventricle	heart
32	chr3:105072400-105072600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
33	chr3:105072400-105072600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr3:105072400-105072600	Flanking Active TSS	NHLF	lung
35	chr3:105072400-105072800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:105072400-105072800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:105072400-105072800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:105072400-105072800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:105072400-105072800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr3:105072400-105072800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:105072400-105072800	Flanking Active TSS	Aorta	Aorta
42	chr3:105072400-105072800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
43	chr3:105072400-105072800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
44	chr3:105072400-105072800	Active TSS	Placenta	Placenta
45	chr3:105072400-105072800	Enhancers	Lung	lung
46	chr3:105072400-105072800	Active TSS	Psoas Muscle	Psoas
47	chr3:105072400-105073000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:105072400-105073000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr3:105072400-105073000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
50	chr3:105072400-105073000	Active TSS	Cortex derived primary cultured neurospheres	brain

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