Variant report

Variant	rs28404401
Chromosome Location	chr8:92029608-92029609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:92029069..92031274-chr8:92031690..92034648,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1002583	0.87[EUR][1000 genomes]
rs10106570	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1038545	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1038546	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1055146	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10808632	0.82[EUR][1000 genomes]
rs10808633	0.82[EUR][1000 genomes]
rs10808634	0.82[EUR][1000 genomes]
rs1159962	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1160329	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11780153	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1386113	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1471847	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1486464	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1486468	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1552397	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1825691	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1973282	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1973283	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2019889	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2035595	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2054806	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2101378	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631007	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631008	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2631011	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2631013	0.80[AMR][1000 genomes]
rs2631015	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2631018	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631023	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631025	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631026	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631029	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631031	0.83[EUR][1000 genomes]
rs2631032	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2677572	0.84[ASN][1000 genomes]
rs2677574	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2677581	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2740772	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2740773	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2740774	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2740775	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2740776	0.81[AMR][1000 genomes]
rs2740778	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2740779	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2740780	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2740781	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2740784	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2740785	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2740788	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2740791	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2740796	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2740798	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2740801	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2740802	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28618232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28675099	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34213675	0.80[AFR][1000 genomes]
rs35972814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4529427	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664410	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7818155	0.84[AMR][1000 genomes]
rs7818187	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828122	0.84[AMR][1000 genomes]
rs7831333	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7832881	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7837376	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931336	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs931337	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs997898	0.82[EUR][1000 genomes]
rs997899	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028628	chr8:91680968-92418954	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539672	chr8:91680968-92418954	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv891185	chr8:91923776-92056288	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2758623	chr8:91974499-92273724	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv2759629	chr8:91974499-92273724	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv1851089	chr8:92006663-92038304	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:91998200-92030200	Weak transcription	Aorta	Aorta
2	chr8:91998200-92030200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr8:91998400-92030200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:91998600-92030000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:91998600-92030200	Weak transcription	Fetal Stomach	stomach
6	chr8:91998600-92030200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:91998600-92030400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:92003800-92040200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr8:92009000-92030200	Weak transcription	Brain Angular Gyrus	brain
10	chr8:92013400-92030200	Weak transcription	Lung	lung
11	chr8:92014600-92033000	Weak transcription	Fetal Intestine Small	intestine
12	chr8:92014800-92032400	Weak transcription	Spleen	Spleen
13	chr8:92015800-92052200	Weak transcription	Pancreas	Pancrea
14	chr8:92023600-92045600	Weak transcription	Right Ventricle	heart
15	chr8:92024400-92030200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr8:92025200-92032400	Strong transcription	Placenta	Placenta
17	chr8:92025400-92032600	Strong transcription	Fetal Thymus	thymus
18	chr8:92026000-92038400	Weak transcription	Esophagus	oesophagus
19	chr8:92026200-92030600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr8:92026200-92031000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr8:92026200-92031800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr8:92026400-92030800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr8:92026400-92032200	Strong transcription	Thymus	Thymus
24	chr8:92026400-92032400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr8:92026400-92032600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr8:92026600-92030800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr8:92026800-92032400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr8:92027000-92031400	Strong transcription	Osteobl	bone
29	chr8:92027200-92032000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr8:92027200-92032200	Strong transcription	Left Ventricle	heart
31	chr8:92027400-92031600	Strong transcription	A549	lung
32	chr8:92027400-92032200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr8:92027600-92030200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:92027800-92030000	Weak transcription	Fetal Muscle Leg	muscle
35	chr8:92027800-92030200	Weak transcription	Fetal Kidney	kidney
36	chr8:92027800-92031000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr8:92027800-92032200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr8:92027800-92033400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr8:92028000-92030200	Weak transcription	Ovary	ovary
40	chr8:92028000-92030400	Weak transcription	Liver	Liver
41	chr8:92028000-92032200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr8:92028000-92032200	Weak transcription	Fetal Intestine Large	intestine
43	chr8:92028000-92032600	Strong transcription	Adipose Nuclei	Adipose
44	chr8:92028000-92032800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr8:92028000-92034400	Weak transcription	Small Intestine	intestine
46	chr8:92028000-92035200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr8:92028000-92036200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr8:92028000-92038000	Weak transcription	Brain Germinal Matrix	brain
49	chr8:92028000-92038000	Weak transcription	Psoas Muscle	Psoas
50	chr8:92028200-92030200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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