Variant report

Variant	rs16956801
Chromosome Location	chr15:31792591-31792592
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1075232	0.82[ASN][1000 genomes]
rs11858516	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12438318	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs12438482	0.93[ASN][1000 genomes]
rs12440108	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12441163	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956707	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs16956738	0.81[ASN][1000 genomes]
rs16956797	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956838	0.86[ASN][1000 genomes]
rs56249651	0.84[ASN][1000 genomes]
rs57491435	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57924788	0.82[ASN][1000 genomes]
rs58156651	0.82[ASN][1000 genomes]
rs60333545	0.90[ASN][1000 genomes]
rs66581165	0.82[ASN][1000 genomes]
rs67216354	0.84[ASN][1000 genomes]
rs67634762	0.82[ASN][1000 genomes]
rs67699697	0.84[ASN][1000 genomes]
rs7166243	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724938	0.82[ASN][1000 genomes]
rs72724958	0.82[ASN][1000 genomes]
rs72724993	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724997	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	87 gene(s)	inside rSNPs	diseases
3	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1046271	chr15:31741255-31795961	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv903845	chr15:31751664-31939001	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv817679	chr15:31787108-31795199	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16956801	ATP10A	cis	parietal	SCAN
rs16956801	TMEM204	trans	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31782400-31821000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:31785400-31794800	Weak transcription	Ovary	ovary
3	chr15:31786600-31800400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:31787200-31810800	Weak transcription	Pancreas	Pancrea
5	chr15:31787400-31793800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:31788000-31792600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:31789000-31793000	Weak transcription	Fetal Brain Female	brain
8	chr15:31789600-31796200	Strong transcription	Brain Substantia Nigra	brain
9	chr15:31790000-31796200	Strong transcription	Brain Anterior Caudate	brain
10	chr15:31790400-31795200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:31791600-31793000	Enhancers	Right Ventricle	heart
12	chr15:31791600-31793200	Enhancers	GM12878-XiMat	blood
13	chr15:31791600-31797000	Strong transcription	Brain Cingulate Gyrus	brain
14	chr15:31791800-31792600	Weak transcription	Esophagus	oesophagus
15	chr15:31791800-31793200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:31791800-31793200	Enhancers	Placenta	Placenta
17	chr15:31791800-31793200	Enhancers	Lung	lung
18	chr15:31791800-31793400	Enhancers	Fetal Muscle Leg	muscle
19	chr15:31791800-31793400	Enhancers	NHDF-Ad	bronchial
20	chr15:31791800-31794000	Enhancers	Left Ventricle	heart
21	chr15:31791800-31795600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:31791800-31796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:31791800-31796600	Weak transcription	HMEC	breast
24	chr15:31792000-31793200	Enhancers	Fetal Stomach	stomach
25	chr15:31792000-31793200	Enhancers	Spleen	Spleen
26	chr15:31792000-31794400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr15:31792000-31796000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:31792200-31792600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:31792200-31792800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:31792200-31793000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr15:31792200-31795000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:31792400-31792600	Enhancers	Primary hematopoietic stem cells	blood
33	chr15:31792400-31792600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr15:31792400-31792800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:31792400-31793200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr15:31792400-31793400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:31792400-31796200	Strong transcription	Brain Hippocampus Middle	brain

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