Variant report

Variant	rs3803369
Chromosome Location	chr15:51375829-51375830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51370657..51374066-chr15:51374474..51376599,3	MCF-7	breast:
2	chr15:51333166..51334706-chr15:51374735..51377031,2	MCF-7	breast:
3	chr15:51374735..51377659-chr15:51385754..51389535,3	MCF-7	breast:
4	chr15:51374848..51376574-chr15:51377965..51380403,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10468000	0.92[ASN][1000 genomes]
rs10468001	0.92[ASN][1000 genomes]
rs11070815	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11631037	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11632323	0.92[ASN][1000 genomes]
rs11633226	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11635054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12439323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441319	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12901289	0.92[ASN][1000 genomes]
rs1550334	0.92[ASN][1000 genomes]
rs1550339	0.92[ASN][1000 genomes]
rs1595584	0.92[ASN][1000 genomes]
rs16963977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1866417	0.92[ASN][1000 genomes]
rs2414092	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2414093	0.92[ASN][1000 genomes]
rs2619684	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2619685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28755423	0.92[ASN][1000 genomes]
rs28757183	1.00[CHB][hapmap]
rs3759808	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775912	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775914	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775917	0.92[ASN][1000 genomes]
rs4775918	0.92[ASN][1000 genomes]
rs4775919	0.92[ASN][1000 genomes]
rs6493484	0.92[ASN][1000 genomes]
rs7170736	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs720316	0.92[ASN][1000 genomes]
rs72742362	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72742383	0.88[EUR][1000 genomes]
rs72744339	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7498099	0.92[ASN][1000 genomes]
rs8035909	0.92[ASN][1000 genomes]
rs893576	0.92[ASN][1000 genomes]
rs934635	0.92[ASN][1000 genomes]
rs9806270	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh 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
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3803369	TRPM7	cis	cerebellum	SCAN
rs3803369	GATM	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51344600-51384400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:51369400-51377600	Weak transcription	Aorta	Aorta
3	chr15:51369800-51385600	Weak transcription	Esophagus	oesophagus
4	chr15:51370000-51376200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:51370000-51376600	Weak transcription	NHLF	lung
6	chr15:51370000-51384600	Weak transcription	Colonic Mucosa	Colon
7	chr15:51370200-51378000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:51370400-51380400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:51370400-51385000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:51370600-51378000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:51371200-51376600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:51371400-51376200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:51371400-51381000	Weak transcription	Ovary	ovary
14	chr15:51372800-51376400	Weak transcription	Osteobl	bone
15	chr15:51373000-51376000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:51373000-51376400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:51373000-51377800	Weak transcription	K562	blood
18	chr15:51373000-51378000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:51373200-51381800	Weak transcription	HSMM	muscle
20	chr15:51373600-51379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:51374600-51378400	Weak transcription	HMEC	breast
22	chr15:51375600-51376000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:51375600-51376200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:51375600-51376200	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr15:51375600-51376400	Enhancers	H9 Cell Line	embryonic stem cell
26	chr15:51375600-51376400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr15:51375600-51376400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr15:51375600-51377200	Strong transcription	HUVEC	blood vessel
29	chr15:51375800-51376000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:51375800-51376000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr15:51375800-51376000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:51375800-51376000	Active TSS	Gastric	stomach
33	chr15:51375800-51376000	Genic enhancers	Spleen	Spleen
34	chr15:51375800-51376200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr15:51375800-51376200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:51375800-51376200	Enhancers	Fetal Stomach	stomach
37	chr15:51375800-51376400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr15:51375800-51376400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr15:51375800-51376800	Enhancers	Stomach Mucosa	stomach
40	chr15:51375800-51377000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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