Variant report

Variant	rs4533618
Chromosome Location	chr3:134033585-134033586
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
2	chr3:134032429..134034030-chr3:134195239..134197108,2	MCF-7	breast:
3	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
4	chr3:134033082..134035437-chr3:134182333..134184840,3	MCF-7	breast:
5	chr3:134027625..134034860-chr3:134199305..134206618,11	MCF-7	breast:
6	chr3:134032463..134034261-chr3:134088924..134090604,2	K562	blood:

Variant related genes	Relation type
ENSG00000182923	Chromatin interaction
ENSG00000260633	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000214289	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13094988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1344687	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270733	0.97[ASN][1000 genomes]
rs2400273	1.00[JPT][hapmap]
rs34426406	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34591691	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596580	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688449	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913236	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160848	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35369871	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131649	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131651	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234420	0.97[ASN][1000 genomes]
rs4270476	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4437113	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4449291	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4470481	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504146	0.85[ASN][1000 genomes]
rs4510358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4558731	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4574266	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682661	0.97[ASN][1000 genomes]
rs4682663	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55721085	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6774600	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810377	1.00[JPT][hapmap]
rs71331752	0.95[ASN][1000 genomes]
rs7431754	0.97[ASN][1000 genomes]
rs7614238	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621320	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641605	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644134	0.95[ASN][1000 genomes]
rs7652144	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289467	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843732	1.00[JPT][hapmap]
rs9863226	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9866886	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4533618	TMEM22	cis	parietal	SCAN
rs4533618	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4533618	FOXL2	cis	parietal	SCAN
rs4533618	RBP1	cis	parietal	SCAN
rs4533618	RP11-375I20.6	cis	Thyroid	GTEx
rs4533618	BPIL2	trans	parietal	SCAN
rs4533618	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs4533618	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134026800-134034800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:134030000-134037200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:134030200-134034000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:134030800-134035000	Enhancers	Spleen	Spleen
5	chr3:134031600-134033800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:134032000-134033800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:134032200-134034200	Flanking Active TSS	Osteobl	bone
8	chr3:134032400-134033600	Flanking Active TSS	Liver	Liver
9	chr3:134032400-134033600	Flanking Active TSS	NHDF-Ad	bronchial
10	chr3:134032400-134033600	Flanking Active TSS	NHLF	lung
11	chr3:134032400-134034000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr3:134032400-134034200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr3:134032400-134034200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr3:134032600-134033800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr3:134032600-134034200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:134032800-134033600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:134032800-134033800	Enhancers	Fetal Lung	lung
18	chr3:134032800-134034000	Enhancers	Brain Angular Gyrus	brain
19	chr3:134032800-134034000	Enhancers	Gastric	stomach
20	chr3:134032800-134034200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
21	chr3:134032800-134034200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr3:134032800-134034200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:134032800-134034200	Flanking Active TSS	A549	lung
24	chr3:134032800-134034400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr3:134032800-134034600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:134032800-134034800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr3:134032800-134034800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:134032800-134034800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:134032800-134034800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:134032800-134034800	Enhancers	Brain Substantia Nigra	brain
31	chr3:134032800-134034800	Enhancers	Lung	lung
32	chr3:134032800-134034800	Enhancers	Ovary	ovary
33	chr3:134032800-134034800	Enhancers	Pancreas	Pancrea
34	chr3:134032800-134034800	Enhancers	Psoas Muscle	Psoas
35	chr3:134032800-134035000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:134032800-134035000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:134032800-134035000	Enhancers	Fetal Muscle Leg	muscle
38	chr3:134032800-134035000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr3:134032800-134035000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:134032800-134035200	Enhancers	Brain Hippocampus Middle	brain
41	chr3:134033000-134033600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:134033000-134033600	Enhancers	Fetal Kidney	kidney
43	chr3:134033000-134033600	Enhancers	HUVEC	blood vessel
44	chr3:134033000-134033800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
45	chr3:134033000-134033800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:134033000-134033800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
47	chr3:134033000-134034000	Enhancers	NH-A	brain
48	chr3:134033000-134034200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
49	chr3:134033000-134034200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr3:134033000-134034200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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