Variant report

Variant	rs4799629
Chromosome Location	chr18:29669761-29669762
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	chr18:29598038..29600342-chr18:29668214..29669893,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101695	Chromatin interaction
ENSG00000263917	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1054667	0.82[GIH][hapmap]
rs11081741	0.82[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11081746	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11663563	0.89[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs12458548	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12458837	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12458851	0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12604223	0.80[AMR][1000 genomes]
rs12605137	0.89[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1808891	0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2018380	0.82[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs2048245	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs3760568	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4799326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4799632	0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62093949	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62093950	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7238559	0.88[AMR][1000 genomes]
rs9676102	0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs993897	0.83[AMR][1000 genomes];0.81[EUR][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	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv909521	chr18:29645496-29671510	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv909522	chr18:29645496-29674992	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4799629	RNF138	cis	multi-tissue	Pritchard
rs4799629	RNF138	cis	Esophagus Mucosa	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29631400-29671400	Weak transcription	Hela-S3	cervix
2	chr18:29656000-29671400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:29663800-29671400	Weak transcription	Fetal Kidney	kidney
4	chr18:29664400-29671400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:29664600-29671600	Weak transcription	Left Ventricle	heart
6	chr18:29665200-29671400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr18:29665200-29671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr18:29665400-29671400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr18:29665600-29671400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr18:29665600-29671400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr18:29666000-29670800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr18:29666000-29671400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr18:29666000-29671400	Weak transcription	NHDF-Ad	bronchial
14	chr18:29666200-29670800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr18:29666200-29671400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr18:29666200-29671400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr18:29666200-29671400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr18:29666400-29670800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr18:29666400-29670800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr18:29666400-29671000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr18:29666400-29671200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr18:29666400-29671200	Weak transcription	HUVEC	blood vessel
23	chr18:29666400-29671400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr18:29666400-29671400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr18:29666400-29671400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr18:29666400-29671400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr18:29666400-29671400	Weak transcription	Adipose Nuclei	Adipose
28	chr18:29666400-29671400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr18:29666400-29671400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr18:29666400-29671400	Weak transcription	Thymus	Thymus
31	chr18:29666400-29671400	Weak transcription	Dnd41	blood
32	chr18:29666600-29670800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr18:29666600-29671000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr18:29666600-29671200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr18:29666600-29671200	Weak transcription	Fetal Thymus	thymus
36	chr18:29666600-29671400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr18:29666600-29671400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr18:29666600-29671400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr18:29666600-29671400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr18:29667000-29671000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr18:29667000-29671400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr18:29667200-29671400	Weak transcription	NHLF	lung
43	chr18:29667200-29671600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:29667200-29671600	Weak transcription	Stomach Mucosa	stomach
45	chr18:29667400-29671200	Weak transcription	Fetal Muscle Leg	muscle
46	chr18:29667400-29671400	Weak transcription	Osteobl	bone
47	chr18:29667600-29671400	Weak transcription	HMEC	breast
48	chr18:29667600-29671400	Weak transcription	NH-A	brain
49	chr18:29667600-29671400	Weak transcription	NHEK	skin
50	chr18:29667600-29671600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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