Variant report

Variant	rs16831388
Chromosome Location	chr1:160095625-160095626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:160094059-160096024	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:160095470-160096015	U87	brain:	n/a	n/a
3	POLR2A	chr1:160095449-160095979	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160093121..160095812-chr1:160107178..160109878,2	K562	blood:
2	chr1:160094674..160096214-chr1:160096674..160098253,2	MCF-7	breast:

Variant related genes	Relation type
ATP1A2	TF binding region
ENSG00000018625	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1046995	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10494336	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1063125	0.86[ASN][1000 genomes]
rs10908761	0.82[ASN][1000 genomes]
rs12136519	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831438	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs16831441	0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17846707	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070702	0.88[ASN][1000 genomes]
rs2070703	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2070704	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2753267	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs3747625	0.88[ASN][1000 genomes]
rs55967674	0.83[ASN][1000 genomes]
rs56199408	0.87[ASN][1000 genomes]
rs58313172	0.96[ASN][1000 genomes]
rs9660305	0.96[ASN][1000 genomes]
rs9661252	0.92[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	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription 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	38 gene(s)	inside rSNPs	diseases
10	nsv872490	chr1:160083012-160121488	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs16831388	ATP1A4	cis	Esophagus Muscularis	GTEx
rs16831388	INSRR	cis	parietal	SCAN
rs16831388	ATF6	cis	cerebellum	SCAN
rs16831388	ATP1A4	cis	Muscle Skeletal	GTEx
rs16831388	ATP1A4	cis	Artery Tibial	GTEx
rs16831388	DEDD	cis	cerebellum	SCAN
rs16831388	ATP1A4	cis	Artery Aorta	GTEx
rs16831388	ATP1A4	cis	Heart Left Ventricle	GTEx
rs16831388	GON4L	cis	cerebellum	SCAN
rs16831388	FCRL4	cis	cerebellum	SCAN
rs16831388	NDUFS2	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160088000-160097200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:160088000-160146200	Weak transcription	Spleen	Spleen
3	chr1:160088800-160107400	Weak transcription	Fetal Brain Female	brain
4	chr1:160089000-160097400	Weak transcription	Ovary	ovary
5	chr1:160090200-160104600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:160090600-160112600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:160092000-160097200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:160092400-160095800	Genic enhancers	Left Ventricle	heart
9	chr1:160092400-160095800	Enhancers	Psoas Muscle	Psoas
10	chr1:160092400-160112200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:160092800-160095800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:160092800-160095800	Enhancers	Right Atrium	heart
13	chr1:160092800-160100800	Strong transcription	Fetal Stomach	stomach
14	chr1:160093000-160095800	Enhancers	Esophagus	oesophagus
15	chr1:160093000-160095800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
16	chr1:160093000-160096000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:160093000-160096400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:160093000-160098600	Enhancers	Placenta	Placenta
19	chr1:160093200-160095800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:160093200-160095800	Enhancers	NHEK	skin
21	chr1:160093400-160096000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:160093400-160098000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:160093600-160099800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:160093800-160095800	Genic enhancers	Aorta	Aorta
25	chr1:160093800-160096000	Enhancers	HMEC	breast
26	chr1:160093800-160096000	Enhancers	NHDF-Ad	bronchial
27	chr1:160093800-160096200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:160093800-160096200	Enhancers	Adipose Nuclei	Adipose
29	chr1:160093800-160096800	Weak transcription	Brain Substantia Nigra	brain
30	chr1:160093800-160098400	Enhancers	HepG2	liver
31	chr1:160093800-160101200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:160093800-160101800	Weak transcription	Gastric	stomach
33	chr1:160093800-160106600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:160094000-160095800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:160094000-160095800	Enhancers	NHLF	lung
36	chr1:160094000-160096000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:160094000-160096000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:160094000-160096400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:160094000-160096400	Enhancers	Osteobl	bone
40	chr1:160094000-160097400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:160094000-160112000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:160094200-160095800	Enhancers	Fetal Intestine Large	intestine
43	chr1:160094200-160096000	Enhancers	NH-A	brain
44	chr1:160094200-160096400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:160094200-160096400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:160094400-160096000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:160094400-160096000	Enhancers	Fetal Intestine Small	intestine
48	chr1:160094400-160096600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:160094400-160097200	Weak transcription	Pancreas	Pancrea
50	chr1:160094600-160097200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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