Variant report

Variant	rs325392
Chromosome Location	chr15:100237682-100237683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1019974	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11247119	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12592092	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593522	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12593785	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595285	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912791	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs12916000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1434232	0.82[ASW][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap]
rs167805	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs170521	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191256	0.87[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2033546	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2117309	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2570807	0.86[EUR][1000 genomes]
rs2570808	0.91[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2570816	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2570823	0.80[EUR][1000 genomes]
rs2570825	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2581467	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2581468	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2581470	0.84[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2581472	0.84[EUR][1000 genomes]
rs2862869	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2862870	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28712314	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2902349	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs325381	0.85[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs325390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325394	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs325404	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325409	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325410	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325411	0.82[ASW][hapmap];0.83[MEX][hapmap]
rs325413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34443706	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34756251	0.91[ASN][1000 genomes]
rs34779575	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34981499	0.91[ASN][1000 genomes]
rs35410986	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35441914	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3730281	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424892	0.87[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs4965529	0.83[ASN][1000 genomes]
rs4965532	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162392	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7165899	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs73482408	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7496677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8036535	0.83[YRI][hapmap]
rs892465	1.00[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs897073	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[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	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv904562	chr15:100214935-100237682	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs325392	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100171200-100248800	Weak transcription	Gastric	stomach
3	chr15:100212800-100240000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:100213600-100243400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:100219400-100248200	Weak transcription	Small Intestine	intestine
7	chr15:100219600-100248400	Weak transcription	Spleen	Spleen
8	chr15:100219800-100243600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:100222800-100243600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:100223600-100247400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:100223800-100241000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:100223800-100243600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:100223800-100246800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:100224000-100246600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:100226800-100240000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:100227400-100238200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:100227400-100238400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:100227600-100238600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:100227800-100238200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:100227800-100243600	Weak transcription	HepG2	liver
21	chr15:100228400-100238600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:100228800-100238200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:100230600-100237800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:100231000-100250600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:100231400-100244200	Weak transcription	Stomach Mucosa	stomach
26	chr15:100233200-100243200	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:100233200-100243200	Weak transcription	A549	lung
28	chr15:100233200-100243200	Weak transcription	NHLF	lung
29	chr15:100233200-100246800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:100233400-100240600	Weak transcription	Brain Substantia Nigra	brain
31	chr15:100233400-100240600	Weak transcription	Right Atrium	heart
32	chr15:100233400-100243400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:100233400-100243600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:100233400-100244200	Weak transcription	Aorta	Aorta
35	chr15:100233400-100244200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:100233400-100244400	Weak transcription	Thymus	Thymus
37	chr15:100233400-100247000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:100233400-100247000	Weak transcription	Fetal Stomach	stomach
39	chr15:100233400-100247000	Weak transcription	Left Ventricle	heart
40	chr15:100233400-100247200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:100233400-100247400	Weak transcription	Psoas Muscle	Psoas
42	chr15:100233400-100247600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:100233400-100248400	Weak transcription	Right Ventricle	heart
44	chr15:100233400-100248800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:100233400-100248800	Weak transcription	Esophagus	oesophagus
46	chr15:100233400-100248800	Weak transcription	Fetal Intestine Small	intestine
47	chr15:100233400-100248800	Weak transcription	Lung	lung
48	chr15:100233400-100248800	Weak transcription	Ovary	ovary
49	chr15:100233400-100248800	Weak transcription	Pancreas	Pancrea
50	chr15:100233400-100250600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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