Variant report

Variant	rs827105
Chromosome Location	chr3:158078400-158078401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1095625	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095631	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095632	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103981	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915781	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193519	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369561	1.00[CEU][hapmap]
rs1435637	0.83[EUR][1000 genomes]
rs1520657	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520662	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520666	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625612	0.96[EUR][1000 genomes]
rs1656360	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656362	0.98[EUR][1000 genomes]
rs1656367	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1656371	0.98[EUR][1000 genomes]
rs1714505	1.00[CEU][hapmap]
rs1714508	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1714510	0.98[EUR][1000 genomes]
rs1714512	0.93[EUR][1000 genomes]
rs1714513	0.90[EUR][1000 genomes]
rs1714517	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1714526	0.98[EUR][1000 genomes]
rs1724650	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724725	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs1730038	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956471	0.93[EUR][1000 genomes]
rs6441191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779266	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788695	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804180	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs698978	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170371	0.92[EUR][1000 genomes]
rs7651712	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827103	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827115	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827116	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827117	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827119	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827133	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827138	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827152	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827182	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827183	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827189	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][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	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
6	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs827105	RSRC1	cis	normal skin	skin_eQTL
rs827105	RSRC1	cis	lesional skin	skin_eQTL
rs827105	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs827105	RSRC1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158048200-158079400	Weak transcription	Right Ventricle	heart
2	chr3:158055200-158086000	Weak transcription	Left Ventricle	heart
3	chr3:158057800-158079600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:158073600-158079400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:158075800-158078400	Weak transcription	Esophagus	oesophagus
6	chr3:158076200-158078600	ZNF genes & repeats	Dnd41	blood
7	chr3:158076200-158087000	Weak transcription	Aorta	Aorta
8	chr3:158076400-158078600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:158076400-158079800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:158076600-158078800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:158076600-158079000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:158076800-158078800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:158076800-158079200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:158077000-158079200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:158077200-158078400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr3:158077200-158078400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:158077200-158078400	ZNF genes & repeats	Lung	lung
18	chr3:158077200-158078400	ZNF genes & repeats	Ovary	ovary
19	chr3:158077200-158078400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr3:158077200-158078600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:158077200-158078600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr3:158077200-158078600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:158077200-158078600	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr3:158077200-158078800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
25	chr3:158077200-158079400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:158077400-158078400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
27	chr3:158077400-158078400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:158077400-158078400	Strong transcription	Adipose Nuclei	Adipose
29	chr3:158077400-158078600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:158077400-158078600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:158077400-158078600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr3:158077400-158078800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:158077400-158078800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:158077600-158079200	ZNF genes & repeats	Spleen	Spleen
35	chr3:158077800-158078400	Strong transcription	Gastric	stomach
36	chr3:158077800-158078800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr3:158077800-158079000	ZNF genes & repeats	Fetal Stomach	stomach
38	chr3:158077800-158079400	Weak transcription	Primary T cells from cord blood	blood
39	chr3:158078000-158079600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:158078200-158079200	Strong transcription	Primary B cells from cord blood	blood
41	chr3:158078200-158079800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:158078200-158081200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:158078400-158078800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:158078400-158078800	Weak transcription	Ovary	ovary
45	chr3:158078400-158079200	ZNF genes & repeats	Esophagus	oesophagus
46	chr3:158078400-158080000	Weak transcription	Adipose Nuclei	Adipose
47	chr3:158078400-158080600	Weak transcription	Gastric	stomach

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