Variant report

Variant	rs827189
Chromosome Location	chr3:158047829-158047830
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	chr3:158046999..158049118-chr3:158139180..158140749,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1095625	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095631	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095632	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103981	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915781	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193519	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369561	1.00[CEU][hapmap]
rs1435637	0.81[EUR][1000 genomes]
rs1520657	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520662	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520666	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625612	0.95[EUR][1000 genomes]
rs1656360	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656362	0.96[EUR][1000 genomes]
rs1656367	0.96[EUR][1000 genomes]
rs1656371	0.96[EUR][1000 genomes]
rs1714505	1.00[CEU][hapmap]
rs1714508	0.96[EUR][1000 genomes]
rs1714510	0.96[EUR][1000 genomes]
rs1714512	0.91[EUR][1000 genomes]
rs1714513	0.88[EUR][1000 genomes]
rs1714517	0.96[EUR][1000 genomes]
rs1714526	0.96[EUR][1000 genomes]
rs1724650	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724725	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1730038	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956471	0.91[EUR][1000 genomes]
rs4680416	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441191	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779266	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788695	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804180	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs698978	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170371	0.90[EUR][1000 genomes]
rs7651712	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827103	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827105	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827107	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827115	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827116	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827117	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827119	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827133	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827138	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827152	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827182	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827183	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845600	0.89[EUR][1000 genomes];1.00[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs827189	RSRC1	cis	uninvolved skin	skin_eQTL
rs827189	RSRC1	cis	normal skin	skin_eQTL
rs827189	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs827189	RSRC1	cis	lesional skin	skin_eQTL

Chromatin state (count:59 , 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	chr3:158047200-158048000	Active TSS	Brain Angular Gyrus	brain
5	chr3:158047200-158048000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr3:158047200-158048000	Active TSS	Right Atrium	heart
7	chr3:158047200-158048200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:158047200-158048200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:158047200-158048200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:158047200-158048200	Active TSS	Fetal Intestine Small	intestine
11	chr3:158047200-158048200	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:158047400-158048000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:158047400-158048000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:158047400-158048000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:158047400-158048000	Active TSS	Brain Anterior Caudate	brain
16	chr3:158047400-158048000	Active TSS	Colonic Mucosa	Colon
17	chr3:158047400-158048000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr3:158047400-158048000	Active TSS	Fetal Muscle Trunk	muscle
19	chr3:158047400-158048000	Active TSS	Fetal Stomach	stomach
20	chr3:158047400-158048000	Active TSS	Left Ventricle	heart
21	chr3:158047400-158048200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:158047400-158048200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:158047400-158048200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:158047400-158048200	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr3:158047400-158048200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:158047400-158048200	Active TSS	Brain Germinal Matrix	brain
27	chr3:158047400-158048200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:158047400-158048200	Active TSS	Fetal Brain Female	brain
29	chr3:158047400-158048400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:158047400-158048600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr3:158047600-158048000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr3:158047600-158048000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:158047600-158048000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:158047600-158048000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:158047600-158048000	Active TSS	Adipose Nuclei	Adipose
36	chr3:158047600-158048000	Active TSS	Brain Cingulate Gyrus	brain
37	chr3:158047600-158048000	Flanking Active TSS	Esophagus	oesophagus
38	chr3:158047600-158048000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr3:158047600-158048000	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr3:158047600-158048000	Active TSS	Right Ventricle	heart
41	chr3:158047600-158048000	Active TSS	NHDF-Ad	bronchial
42	chr3:158047600-158048200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:158047600-158048200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr3:158047600-158048200	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:158047600-158048200	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr3:158047600-158048200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:158047600-158048200	Active TSS	Fetal Intestine Large	intestine
48	chr3:158047600-158048200	Active TSS	Fetal Lung	lung
49	chr3:158047600-158048400	Active TSS	Fetal Heart	heart
50	chr3:158047600-158048400	Active TSS	Fetal Kidney	kidney

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