Variant report

Variant	rs4974495
Chromosome Location	chr3:134059270-134059271
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134031213..134035337-chr3:134058178..134060901,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMOTL2-2	chr3:134058753-134059334	XLOC_003261

Variant related genes	Relation type
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10755085	1.00[CHB][hapmap]
rs1111516	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708815	0.90[ASN][1000 genomes]
rs11719057	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13075185	0.90[ASN][1000 genomes]
rs13322269	0.89[CHB][hapmap]
rs1353776	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1353778	1.00[CHB][hapmap]
rs1466827	0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1498731	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603824	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133307	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303635	0.88[CHB][hapmap]
rs2400278	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400280	0.93[ASN][1000 genomes]
rs34341902	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951257	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773820	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3821705	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974485	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974487	0.84[ASN][1000 genomes]
rs4974489	0.95[ASN][1000 genomes]
rs4974491	0.95[ASN][1000 genomes]
rs4974494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974496	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974497	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974498	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439477	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439478	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.95[ASN][1000 genomes]
rs7613066	0.90[ASN][1000 genomes]
rs9450	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817900	0.95[ASN][1000 genomes]
rs9853621	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4974495	RP11-375I20.6	cis	Heart Left Ventricle	GTEx
rs4974495	RP11-375I20.6	cis	Artery Tibial	GTEx
rs4974495	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs4974495	RP11-375I20.6	cis	Thyroid	GTEx
rs4974495	RP11-375I20.6	cis	lung	GTEx
rs4974495	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4974495	RP11-375I20.6	cis	Artery Aorta	GTEx
rs4974495	FOXL2	cis	parietal	SCAN
rs4974495	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs4974495	TMEM22	cis	parietal	SCAN
rs4974495	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134042000-134060800	Enhancers	Placenta	Placenta
2	chr3:134049200-134060800	Enhancers	Fetal Intestine Large	intestine
3	chr3:134050600-134060400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:134050800-134061000	Weak transcription	Fetal Brain Female	brain
5	chr3:134053000-134061200	Enhancers	Adipose Nuclei	Adipose
6	chr3:134054000-134059600	Weak transcription	Colonic Mucosa	Colon
7	chr3:134054000-134064200	Weak transcription	Aorta	Aorta
8	chr3:134054200-134060200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:134054200-134069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:134054400-134069400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:134054600-134061000	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:134055200-134061400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:134055600-134059600	Weak transcription	HSMM	muscle
14	chr3:134055800-134059400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:134055800-134059600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:134055800-134071000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:134056200-134066600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:134056400-134059600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:134056400-134059600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:134056400-134064800	Weak transcription	Ovary	ovary
21	chr3:134056600-134059600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:134056600-134059800	Weak transcription	HMEC	breast
23	chr3:134056600-134060000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:134056600-134060000	Weak transcription	NHEK	skin
25	chr3:134057200-134060200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:134057200-134067400	Weak transcription	Fetal Heart	heart
27	chr3:134057400-134059800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:134057400-134060800	Enhancers	Fetal Intestine Small	intestine
29	chr3:134057600-134063400	Weak transcription	Pancreas	Pancrea
30	chr3:134058000-134060800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:134058200-134060400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:134058200-134060400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:134058200-134061200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:134058400-134059800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:134058400-134061000	Enhancers	NHDF-Ad	bronchial
36	chr3:134058400-134065000	Weak transcription	Gastric	stomach
37	chr3:134058400-134065200	Weak transcription	Right Ventricle	heart
38	chr3:134058600-134059600	Weak transcription	Esophagus	oesophagus
39	chr3:134058600-134060000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:134058600-134069200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:134058800-134059400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:134058800-134059400	Enhancers	Right Atrium	heart
43	chr3:134058800-134060200	Weak transcription	Spleen	Spleen
44	chr3:134058800-134060400	Enhancers	NHLF	lung
45	chr3:134058800-134060600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:134058800-134060600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:134058800-134060600	Enhancers	Osteobl	bone
48	chr3:134058800-134060800	Enhancers	Fetal Kidney	kidney
49	chr3:134058800-134061200	Enhancers	Fetal Stomach	stomach
50	chr3:134058800-134062600	Strong transcription	Liver	Liver

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