Variant report

Variant	rs6806551
Chromosome Location	chr3:142766776-142766777
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142760714..142763385-chr3:142766244..142768333,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10413	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1043898	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10451867	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10513184	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1053950	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10790	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935475	0.91[EUR][1000 genomes]
rs10935479	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915462	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11922201	0.88[EUR][1000 genomes]
rs12485790	0.85[EUR][1000 genomes]
rs12490776	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12492904	0.91[EUR][1000 genomes]
rs12695770	0.86[EUR][1000 genomes]
rs13075955	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13088422	0.86[EUR][1000 genomes]
rs13094293	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13099995	0.87[EUR][1000 genomes]
rs1349262	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13715	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1375814	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1449868	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1449869	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1530753	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1532588	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1545597	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17557029	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1814565	0.88[EUR][1000 genomes]
rs1827159	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1839406	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1868569	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868570	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1965343	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2045306	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2124541	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2124542	0.91[EUR][1000 genomes]
rs2124543	0.91[EUR][1000 genomes]
rs2137586	0.91[EUR][1000 genomes]
rs2175739	0.91[EUR][1000 genomes]
rs2290549	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353408	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353409	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2353411	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821645	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3856697	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3902877	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4030582	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683444	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683721	0.92[EUR][1000 genomes]
rs4683722	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683723	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4683724	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56382522	0.90[EUR][1000 genomes]
rs6440129	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440131	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440132	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440133	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440134	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6770102	0.91[EUR][1000 genomes]
rs6778454	0.91[EUR][1000 genomes]
rs6781080	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6781887	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6783145	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6784200	0.82[EUR][1000 genomes]
rs6796771	0.86[EUR][1000 genomes]
rs6802376	0.83[EUR][1000 genomes]
rs6805417	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808406	0.82[EUR][1000 genomes]
rs6808689	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7611721	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7623532	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7644475	0.85[EUR][1000 genomes]
rs7648143	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7649225	0.92[EUR][1000 genomes]
rs7652745	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766360	0.89[EUR][1000 genomes]
rs936194	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936196	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936197	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937498	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814656	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816317	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820175	0.81[EUR][1000 genomes]
rs9831162	0.82[EUR][1000 genomes]
rs9835348	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9847059	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851353	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862433	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875210	0.83[EUR][1000 genomes]
rs9877128	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9877135	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv513081	chr3:142764339-142767045	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6806551	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
2	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
3	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
4	chr3:142740000-142769200	Weak transcription	Gastric	stomach
5	chr3:142749000-142784200	Weak transcription	Small Intestine	intestine
6	chr3:142749200-142769000	Weak transcription	Right Ventricle	heart
7	chr3:142749200-142779000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:142754200-142769800	Weak transcription	Colonic Mucosa	Colon
9	chr3:142756000-142774400	Weak transcription	Stomach Mucosa	stomach
10	chr3:142756200-142769200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:142761800-142776600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:142762400-142766800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:142762400-142767000	Weak transcription	Fetal Brain Female	brain
14	chr3:142763000-142769400	Weak transcription	NHEK	skin
15	chr3:142763400-142787000	Weak transcription	Spleen	Spleen
16	chr3:142763600-142769200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:142763600-142770000	Weak transcription	NHLF	lung
18	chr3:142763800-142766800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:142763800-142766800	Weak transcription	Lung	lung
20	chr3:142763800-142769200	Weak transcription	HUVEC	blood vessel
21	chr3:142763800-142769400	Weak transcription	HSMMtube	muscle
22	chr3:142763800-142772600	Weak transcription	Psoas Muscle	Psoas
23	chr3:142763800-142773200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:142764000-142766800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:142764000-142769400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:142764200-142767400	Weak transcription	Fetal Intestine Small	intestine
27	chr3:142764200-142769000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:142764200-142784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:142764400-142766800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:142764600-142766800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:142764600-142766800	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:142764600-142766800	Weak transcription	A549	lung
33	chr3:142764600-142766800	Weak transcription	Osteobl	bone
34	chr3:142764600-142769000	Weak transcription	Ovary	ovary
35	chr3:142764600-142769200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:142764600-142772800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:142764600-142775200	Weak transcription	Brain Angular Gyrus	brain
38	chr3:142764800-142766800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:142764800-142766800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:142764800-142766800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:142764800-142766800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:142764800-142766800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:142764800-142766800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:142764800-142766800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:142764800-142766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:142764800-142766800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:142764800-142766800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:142764800-142766800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:142764800-142766800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:142764800-142766800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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