Variant report

Variant	rs1031925
Chromosome Location	chr3:51379274-51379275
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	chr3:51373184..51375093-chr3:51377621..51380061,2	K562	blood:
2	chr3:51367010..51371078-chr3:51375773..51379297,4	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10212250	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs1055429	0.86[AMR][1000 genomes]
rs10865970	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130282	0.88[YRI][hapmap]
rs11130293	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11721253	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12632046	0.84[EUR][1000 genomes]
rs1383251	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1383252	0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs1480353	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1480354	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1480357	1.00[ASW][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs1480358	1.00[ASW][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs1480363	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs1480365	0.84[AFR][1000 genomes]
rs1542574	1.00[CEU][hapmap];0.83[CHD][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1552072	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs1552073	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs1552074	0.92[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051762	0.91[CEU][hapmap];0.83[CHD][hapmap]
rs1904786	0.84[AFR][1000 genomes]
rs2061951	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs2127655	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219890	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2241784	0.82[EUR][1000 genomes]
rs2355941	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs2355942	0.84[AFR][1000 genomes]
rs2883811	0.90[AFR][1000 genomes]
rs34035394	0.90[AFR][1000 genomes]
rs34251985	0.84[AFR][1000 genomes]
rs4244697	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs4301044	1.00[ASW][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap]
rs4328835	0.88[YRI][hapmap]
rs4367101	1.00[ASW][hapmap];0.88[YRI][hapmap]
rs4378999	0.87[YRI][hapmap]
rs4428169	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4453876	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs4528983	0.88[YRI][hapmap]
rs4568177	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs4611808	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687569	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974093	0.84[AFR][1000 genomes]
rs4974095	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs4974097	0.84[AFR][1000 genomes]
rs4974104	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4974105	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974106	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974109	1.00[ASW][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs6445455	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs6445551	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs6445620	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6445622	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6445624	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445628	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6772664	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs6773260	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6777719	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs6779658	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs6793900	0.86[AMR][1000 genomes]
rs6800805	0.84[AFR][1000 genomes]
rs6809080	0.87[YRI][hapmap]
rs7372658	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs751075	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619584	0.82[YRI][hapmap]
rs7625006	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628533	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap]
rs7633708	0.84[CEU][hapmap]
rs7634514	0.84[AFR][1000 genomes]
rs7644957	1.00[ASW][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap]
rs7648012	0.92[CEU][hapmap]
rs922612	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs9311469	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9825454	0.90[AFR][1000 genomes]
rs9855442	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs9855454	1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs9858412	1.00[ASW][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap]
rs9878100	1.00[ASW][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs9883739	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Melanoma	24980573	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1031925	TEX264	cis	Esophagus Muscularis	GTEx
rs1031925	TEX264	cis	Nerve Tibial	GTEx
rs1031925	TEX264	cis	Artery Tibial	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
2	chr3:51376600-51379400	Enhancers	NHLF	lung
3	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:51377000-51379400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:51377400-51379400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:51377400-51380000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:51378000-51379400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:51378000-51379400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:51378000-51379600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:51378000-51379800	Weak transcription	Fetal Brain Female	brain
12	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:51378200-51379400	Enhancers	Placenta	Placenta
14	chr3:51378200-51383000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:51378400-51379400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:51378400-51379600	Enhancers	Osteobl	bone
17	chr3:51378400-51382600	Weak transcription	Spleen	Spleen
18	chr3:51378400-51389800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:51378600-51380000	Enhancers	HSMMtube	muscle
20	chr3:51378600-51383000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:51378800-51379400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:51378800-51379400	Enhancers	A549	lung
24	chr3:51378800-51379600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:51378800-51379600	Enhancers	HSMM	muscle
26	chr3:51378800-51379800	Weak transcription	Aorta	Aorta
27	chr3:51378800-51379800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:51378800-51380000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:51378800-51381000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:51378800-51381200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:51378800-51381400	Weak transcription	Esophagus	oesophagus
32	chr3:51378800-51381600	Weak transcription	Gastric	stomach
33	chr3:51378800-51381600	Weak transcription	Stomach Mucosa	stomach
34	chr3:51378800-51382000	Enhancers	Hela-S3	cervix
35	chr3:51378800-51383800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:51378800-51387400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:51378800-51388000	Weak transcription	Brain Angular Gyrus	brain
38	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
39	chr3:51379000-51379800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:51379000-51379800	Weak transcription	Brain Anterior Caudate	brain
41	chr3:51379000-51380600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:51379000-51381400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:51379000-51381400	Weak transcription	NHEK	skin
44	chr3:51379000-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:51379000-51386000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:51379000-51390200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
49	chr3:51379200-51380800	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:51379200-51381200	Weak transcription	NHDF-Ad	bronchial

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