Variant report

Variant	rs10412888
Chromosome Location	chr19:56987430-56987431
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10409864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425239	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10425729	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4261655	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509998	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7251105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253670	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253817	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7254602	0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259359	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8108715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109617	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10412888	ZNF667	cis	Esophagus Muscularis	GTEx
rs10412888	ZNF837	cis	parietal	SCAN
rs10412888	ZNF667	cis	Muscle Skeletal	GTEx
rs10412888	ZNF460	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56967200-56987600	Weak transcription	Fetal Heart	heart
2	chr19:56969400-56987600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:56972800-56987600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:56981000-56987600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:56981000-56988000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr19:56981400-56987600	ZNF genes & repeats	Ovary	ovary
7	chr19:56982000-56987600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:56983000-56988000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:56983200-56987800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:56983800-56987600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr19:56983800-56987600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr19:56984000-56988000	Weak transcription	Left Ventricle	heart
13	chr19:56984200-56987600	Weak transcription	HSMMtube	muscle
14	chr19:56984400-56987600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:56984400-56987600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:56984600-56988000	Weak transcription	Psoas Muscle	Psoas
17	chr19:56984800-56987600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:56984800-56987800	Weak transcription	Fetal Kidney	kidney
19	chr19:56984800-56988000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:56985400-56987600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:56985400-56990400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:56985400-56991400	ZNF genes & repeats	Liver	Liver
23	chr19:56985600-56987600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:56986000-56987600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:56986000-56988000	Weak transcription	Right Atrium	heart
26	chr19:56986400-56987600	Weak transcription	Primary T cells from cord blood	blood
27	chr19:56986800-56987600	Enhancers	Fetal Brain Male	brain
28	chr19:56986800-56988000	Enhancers	Right Ventricle	heart
29	chr19:56987000-56987800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:56987000-56990000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:56987000-56990400	ZNF genes & repeats	Gastric	stomach
32	chr19:56987200-56987600	Active TSS	Brain Angular Gyrus	brain
33	chr19:56987200-56987600	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr19:56987200-56988000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr19:56987400-56987600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:56987400-56987600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:56987400-56987600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr19:56987400-56987600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr19:56987400-56987600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:56987400-56987600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:56987400-56987600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:56987400-56987600	Active TSS	Fetal Brain Female	brain
43	chr19:56987400-56987600	Enhancers	Fetal Lung	lung
44	chr19:56987400-56987800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr19:56987400-56987800	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr19:56987400-56987800	Enhancers	Fetal Muscle Trunk	muscle
47	chr19:56987400-56987800	Enhancers	Fetal Stomach	stomach
48	chr19:56987400-56988000	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr19:56987400-56988000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr19:56987400-56988000	ZNF genes & repeats	Fetal Thymus	thymus

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