Variant report

Variant	rs28470602
Chromosome Location	chr14:39497237-39497238
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	chr14:39495466..39497265-chr14:39501219..39502819,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1002193	0.82[AMR][1000 genomes]
rs10129762	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10131369	0.82[AMR][1000 genomes]
rs10134166	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10134656	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10135561	0.82[AMR][1000 genomes]
rs10139666	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140763	0.82[AMR][1000 genomes]
rs10141079	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10141081	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141924	0.82[AMR][1000 genomes]
rs10142117	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10142350	0.82[AMR][1000 genomes]
rs10145417	0.82[AMR][1000 genomes]
rs10145476	0.82[AMR][1000 genomes]
rs10148712	0.82[AMR][1000 genomes]
rs10150756	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10151124	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151960	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1040680	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10467711	0.86[AMR][1000 genomes]
rs10483543	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622731	0.82[AMR][1000 genomes]
rs11622968	0.82[AMR][1000 genomes]
rs11623907	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11623945	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11624584	0.82[AMR][1000 genomes]
rs11625689	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11626002	0.82[AMR][1000 genomes]
rs11627264	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11628480	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11628564	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11628784	0.87[EUR][1000 genomes]
rs11845793	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11848067	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11849209	0.82[AMR][1000 genomes]
rs11850579	0.82[AMR][1000 genomes]
rs11851680	0.82[AMR][1000 genomes]
rs12323565	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12587208	0.82[AMR][1000 genomes]
rs12590373	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13021	0.82[AMR][1000 genomes]
rs17092044	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17092050	0.82[AMR][1000 genomes]
rs17108596	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108664	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108696	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17108948	0.82[AMR][1000 genomes]
rs1884384	0.85[ASN][1000 genomes]
rs2025061	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2144528	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2273592	0.82[AMR][1000 genomes]
rs28414518	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28501673	0.82[AMR][1000 genomes]
rs28583114	0.82[AMR][1000 genomes]
rs28666016	0.82[AMR][1000 genomes]
rs28821293	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3896147	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45622837	0.82[AMR][1000 genomes]
rs55672305	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55737943	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56064304	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56105133	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56785762	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57326310	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57482489	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58601678	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59465524	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7144625	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7155307	0.82[AMR][1000 genomes]
rs7159520	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs743223	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs761805	0.82[AMR][1000 genomes]
rs8019396	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs926970	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs993675	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39465600-39498200	Weak transcription	NH-A	brain
2	chr14:39469200-39497400	Weak transcription	HSMM	muscle
3	chr14:39473400-39498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:39479600-39498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:39480200-39499000	Weak transcription	NHDF-Ad	bronchial
6	chr14:39482800-39499200	Weak transcription	Right Ventricle	heart
7	chr14:39485200-39498600	Weak transcription	Aorta	Aorta
8	chr14:39486000-39498600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:39486400-39497400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:39486400-39498600	Weak transcription	HSMMtube	muscle
11	chr14:39486600-39498600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr14:39486800-39498800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:39487000-39498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr14:39487000-39499400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:39487200-39498600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:39487200-39498600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr14:39487200-39508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr14:39491400-39499200	Weak transcription	NHEK	skin
19	chr14:39492000-39498800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:39492600-39498800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr14:39493000-39498000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:39493200-39498400	Weak transcription	Fetal Brain Female	brain
23	chr14:39493400-39497800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr14:39493400-39497800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:39493400-39498800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr14:39493400-39505800	Weak transcription	Psoas Muscle	Psoas
27	chr14:39493600-39498200	Weak transcription	HMEC	breast
28	chr14:39493600-39499000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr14:39493800-39498200	Weak transcription	Primary T cells from cord blood	blood
30	chr14:39493800-39499000	Weak transcription	NHLF	lung
31	chr14:39494000-39498600	Weak transcription	Adipose Nuclei	Adipose
32	chr14:39494000-39498800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:39494400-39497800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:39494800-39498600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr14:39494800-39499000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr14:39494800-39499000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr14:39495000-39497400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:39495000-39498000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr14:39495000-39499000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr14:39495200-39499000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr14:39495400-39498000	Weak transcription	Osteobl	bone
42	chr14:39495400-39498800	Weak transcription	Fetal Muscle Leg	muscle
43	chr14:39495400-39499000	Weak transcription	Brain Hippocampus Middle	brain
44	chr14:39495400-39499000	Weak transcription	Gastric	stomach
45	chr14:39495400-39499000	Weak transcription	Pancreas	Pancrea
46	chr14:39495400-39505000	Weak transcription	Small Intestine	intestine
47	chr14:39495400-39505800	Weak transcription	Fetal Kidney	kidney
48	chr14:39495400-39518200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr14:39495600-39498800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr14:39495600-39498800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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