Variant report

Variant	rs3806329
Chromosome Location	chr1:220863423-220863424
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	chr1:220862132..220866220-chr1:220920879..220923309,4	MCF-7	breast:
2	chr1:220863249..220864128-chr1:220950068..220950638,2	K562	blood:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12032280	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407624	1.00[ASW][hapmap];0.80[CEU][hapmap]
rs12410279	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12563921	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12564479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472253	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1933002	0.85[CHD][hapmap]
rs1933008	0.85[CHD][hapmap]
rs2253641	0.85[CHD][hapmap]
rs337163	0.81[EUR][1000 genomes]
rs337166	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337167	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337168	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337174	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs337182	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs337192	0.81[EUR][1000 genomes]
rs382451	0.83[EUR][1000 genomes]
rs4846658	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59423796	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61830219	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61830238	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6541155	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs6689349	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699189	0.83[CHB][hapmap]
rs72629673	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs774139	0.80[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468194	chr1:220845610-220885612	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv549227	chr1:220845610-220885612	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3806329	C1orf115	cis	cerebellum	SCAN
rs3806329	MOSC1	cis	parietal	SCAN
rs3806329	C1orf115	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220863000-220863600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:220863000-220863600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr1:220863000-220863600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr1:220863000-220863600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr1:220863000-220863600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr1:220863000-220863600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:220863000-220863600	Flanking Active TSS	Brain Substantia Nigra	brain
8	chr1:220863000-220863600	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr1:220863000-220863600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:220863000-220863600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
11	chr1:220863000-220863600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr1:220863000-220863600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr1:220863000-220863600	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
14	chr1:220863000-220864000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:220863000-220864000	Active TSS	Brain Anterior Caudate	brain
16	chr1:220863000-220864600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr1:220863000-220864600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:220863000-220864600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:220863000-220864800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:220863000-220865000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:220863000-220865200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr1:220863000-220865200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:220863000-220865200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:220863000-220865200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr1:220863000-220866000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:220863200-220863600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
31	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
32	chr1:220863200-220863600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
34	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
35	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:220863200-220863600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:220863200-220863600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:220863200-220863600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:220863200-220863600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:220863200-220863600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr1:220863200-220863600	Flanking Active TSS	Liver	Liver
42	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
43	chr1:220863200-220863600	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr1:220863200-220863600	Flanking Active TSS	Esophagus	oesophagus
45	chr1:220863200-220863600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
47	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr1:220863200-220863600	Enhancers	Placenta	Placenta
50	chr1:220863200-220863600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach

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