Variant report

Variant	rs827188
Chromosome Location	chr3:158047753-158047754
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	chr3:158046999..158049118-chr3:158139180..158140749,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1070894	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1095629	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1095630	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1095633	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1095634	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706229	0.85[EUR][1000 genomes]
rs11707696	0.96[ASN][1000 genomes]
rs11719388	0.97[ASN][1000 genomes]
rs1210358	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13060100	0.87[EUR][1000 genomes]
rs13072413	0.87[EUR][1000 genomes]
rs13086348	0.86[EUR][1000 genomes]
rs1581412	0.86[EUR][1000 genomes]
rs1589526	0.87[EUR][1000 genomes]
rs1589528	0.86[EUR][1000 genomes]
rs1608968	0.88[EUR][1000 genomes]
rs1609523	0.86[EUR][1000 genomes]
rs1609524	0.87[EUR][1000 genomes]
rs1610269	0.86[EUR][1000 genomes]
rs1618377	0.91[EUR][1000 genomes]
rs1618381	0.91[AFR][1000 genomes]
rs1624094	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1724676	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1724677	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1724727	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1724728	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1724729	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1729997	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1729999	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1730043	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1730054	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1730100	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682397	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2693528	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2693541	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4261833	0.86[EUR][1000 genomes]
rs4271876	0.86[EUR][1000 genomes]
rs4318510	0.87[EUR][1000 genomes]
rs4320039	0.87[EUR][1000 genomes]
rs4320040	0.87[EUR][1000 genomes]
rs4336069	0.86[EUR][1000 genomes]
rs4396839	0.87[EUR][1000 genomes]
rs4410410	0.88[EUR][1000 genomes]
rs4558712	0.87[EUR][1000 genomes]
rs4561782	0.87[EUR][1000 genomes]
rs4679821	0.87[EUR][1000 genomes]
rs4679823	0.86[EUR][1000 genomes]
rs4680417	0.86[EUR][1000 genomes]
rs4680418	0.85[EUR][1000 genomes]
rs57361244	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441175	0.86[EUR][1000 genomes]
rs6441176	0.87[EUR][1000 genomes]
rs6441177	0.86[EUR][1000 genomes]
rs6762154	0.87[EUR][1000 genomes]
rs6768496	0.85[EUR][1000 genomes]
rs6776109	0.86[EUR][1000 genomes]
rs6777853	0.87[EUR][1000 genomes]
rs6777968	0.87[EUR][1000 genomes]
rs6786057	0.87[EUR][1000 genomes]
rs6787072	0.86[EUR][1000 genomes]
rs6802443	0.87[EUR][1000 genomes]
rs6803342	0.86[EUR][1000 genomes]
rs698980	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs698986	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs698988	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs698989	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs698990	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs698991	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs699916	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs699917	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs699919	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs699921	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs699922	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs699924	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73168795	0.93[ASN][1000 genomes]
rs7614091	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617503	0.87[EUR][1000 genomes]
rs7617666	0.97[ASN][1000 genomes]
rs7621889	0.99[ASN][1000 genomes]
rs7623107	0.86[EUR][1000 genomes]
rs7629341	0.85[EUR][1000 genomes]
rs7629432	0.82[EUR][1000 genomes]
rs7642751	0.85[EUR][1000 genomes]
rs7645383	0.86[EUR][1000 genomes]
rs7645475	0.86[EUR][1000 genomes]
rs7648169	0.85[EUR][1000 genomes]
rs7651288	0.81[EUR][1000 genomes]
rs827090	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs827091	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs827118	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs827120	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs827121	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs827122	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs827123	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs827125	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs827127	0.83[AFR][1000 genomes]
rs827131	0.83[AFR][1000 genomes]
rs827136	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs827143	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827148	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827150	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827151	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827156	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827158	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827159	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827161	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827163	0.88[AFR][1000 genomes]
rs827164	0.83[AFR][1000 genomes]
rs827169	0.83[EUR][1000 genomes]
rs827172	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs827175	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827802	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827803	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827804	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827806	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs827807	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852110	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs862351	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs864859	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9290022	0.88[EUR][1000 genomes]
rs9811346	0.86[EUR][1000 genomes]
rs9814827	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9838196	0.88[EUR][1000 genomes]
rs9840667	0.86[EUR][1000 genomes]
rs9848977	0.86[EUR][1000 genomes]
rs9852745	0.87[EUR][1000 genomes]
rs9855534	0.85[EUR][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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs827188	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157993400-158054600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:158046800-158048200	Active TSS	Duodenum Mucosa	Duodenum
3	chr3:158047000-158055400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr3:158047200-158047800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:158047200-158047800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:158047200-158048000	Active TSS	Brain Angular Gyrus	brain
7	chr3:158047200-158048000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr3:158047200-158048000	Active TSS	Right Atrium	heart
9	chr3:158047200-158048200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:158047200-158048200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:158047200-158048200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:158047200-158048200	Active TSS	Fetal Intestine Small	intestine
13	chr3:158047200-158048200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:158047400-158047800	Active TSS	Ovary	ovary
15	chr3:158047400-158047800	Active TSS	Osteobl	bone
16	chr3:158047400-158048000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:158047400-158048000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:158047400-158048000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr3:158047400-158048000	Active TSS	Brain Anterior Caudate	brain
20	chr3:158047400-158048000	Active TSS	Colonic Mucosa	Colon
21	chr3:158047400-158048000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr3:158047400-158048000	Active TSS	Fetal Muscle Trunk	muscle
23	chr3:158047400-158048000	Active TSS	Fetal Stomach	stomach
24	chr3:158047400-158048000	Active TSS	Left Ventricle	heart
25	chr3:158047400-158048200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr3:158047400-158048200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:158047400-158048200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:158047400-158048200	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr3:158047400-158048200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:158047400-158048200	Active TSS	Brain Germinal Matrix	brain
31	chr3:158047400-158048200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:158047400-158048200	Active TSS	Fetal Brain Female	brain
33	chr3:158047400-158048400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:158047400-158048600	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr3:158047600-158047800	Enhancers	Gastric	stomach
36	chr3:158047600-158047800	Active TSS	Pancreas	Pancrea
37	chr3:158047600-158048000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr3:158047600-158048000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:158047600-158048000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:158047600-158048000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:158047600-158048000	Active TSS	Adipose Nuclei	Adipose
42	chr3:158047600-158048000	Active TSS	Brain Cingulate Gyrus	brain
43	chr3:158047600-158048000	Flanking Active TSS	Esophagus	oesophagus
44	chr3:158047600-158048000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr3:158047600-158048000	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr3:158047600-158048000	Active TSS	Right Ventricle	heart
47	chr3:158047600-158048000	Active TSS	NHDF-Ad	bronchial
48	chr3:158047600-158048200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:158047600-158048200	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr3:158047600-158048200	Active TSS	HUES64 Cell Line	embryonic stem cell

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