Variant report

Variant	rs13100865
Chromosome Location	chr3:120137465-120137466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:120066683..120069850-chr3:120134285..120137656,5	MCF-7	breast:
2	chr3:120066496..120069971-chr3:120134010..120137845,6	MCF-7	breast:
3	chr3:120135734..120138028-chr3:120174472..120177330,2	MCF-7	breast:
4	chr3:120136391..120139340-chr3:120276034..120279006,3	MCF-7	breast:
5	chr3:120137423..120138991-chr3:120276678..120279072,31	MCF-7	breast:
6	chr3:120137444..120138878-chr3:120277379..120278358,9	MCF-7	breast:
7	chr3:120135893..120137729-chr3:120167558..120169629,2	MCF-7	breast:
8	chr3:120136351..120139286-chr3:120156446..120159592,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056928	1.00[JPT][hapmap]
rs1147696	1.00[JPT][hapmap]
rs1147698	1.00[JPT][hapmap]
rs1147699	1.00[JPT][hapmap]
rs12173	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12192	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1259328	1.00[JPT][hapmap]
rs13061630	1.00[JPT][hapmap]
rs13066496	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13070508	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13081675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs13083670	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13088020	0.84[EUR][1000 genomes]
rs13096232	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13096256	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13096973	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097755	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs13709	1.00[JPT][hapmap]
rs1492272	1.00[JPT][hapmap]
rs1515577	1.00[JPT][hapmap]
rs17813772	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes]
rs1969356	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2030414	1.00[JPT][hapmap]
rs2091726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272515	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2488	1.00[JPT][hapmap]
rs33935225	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34446218	0.91[EUR][1000 genomes]
rs34805176	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36001904	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36068602	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755558	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676696	0.88[AMR][1000 genomes]
rs4676698	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4676768	0.90[AMR][1000 genomes]
rs4676776	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4676777	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4676778	1.00[JPT][hapmap]
rs4676779	1.00[JPT][hapmap]
rs4676781	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676783	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56100867	0.91[EUR][1000 genomes]
rs6438575	1.00[ASW][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap]
rs6775963	0.91[EUR][1000 genomes]
rs71327229	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs869247	1.00[JPT][hapmap]
rs9880550	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS 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	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13100865	C3orf1	cis	cerebellum	SCAN
rs13100865	CD80	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
2	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:120128200-120137600	Weak transcription	Gastric	stomach
4	chr3:120135000-120137600	Weak transcription	Lung	lung
5	chr3:120135400-120139400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:120135400-120151600	Genic enhancers	Osteobl	bone
7	chr3:120135600-120141600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:120135800-120138200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:120135800-120138200	Enhancers	Stomach Mucosa	stomach
10	chr3:120135800-120138600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:120136000-120137600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:120136000-120137600	Weak transcription	Spleen	Spleen
13	chr3:120136200-120137600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:120136200-120138000	Weak transcription	Esophagus	oesophagus
15	chr3:120136600-120137600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:120136600-120137600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:120136600-120137600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:120136600-120137600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:120136600-120138200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:120136600-120138200	Enhancers	NH-A	brain
21	chr3:120136800-120137600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:120136800-120137600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:120136800-120137600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:120136800-120137600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:120136800-120137600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:120136800-120137600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:120136800-120137600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:120136800-120137600	Enhancers	Hela-S3	cervix
29	chr3:120136800-120137800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:120136800-120137800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:120136800-120137800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:120136800-120137800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:120136800-120138000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:120136800-120138200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:120136800-120138200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:120136800-120138200	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:120136800-120138200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:120136800-120138200	Enhancers	Liver	Liver
39	chr3:120136800-120138200	Enhancers	Duodenum Mucosa	Duodenum
40	chr3:120136800-120138200	Enhancers	Fetal Intestine Large	intestine
41	chr3:120136800-120138200	Enhancers	A549	lung
42	chr3:120136800-120138200	Enhancers	HMEC	breast
43	chr3:120136800-120138200	Enhancers	NHEK	skin
44	chr3:120136800-120138400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr3:120136800-120138400	Enhancers	Placenta	Placenta
46	chr3:120136800-120138400	Enhancers	Fetal Thymus	thymus
47	chr3:120136800-120138400	Enhancers	NHDF-Ad	bronchial
48	chr3:120136800-120138600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr3:120136800-120138600	Weak transcription	Psoas Muscle	Psoas
50	chr3:120136800-120138800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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