Variant report

Variant	rs12136519
Chromosome Location	chr1:160101119-160101120
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160098805..160101465-chr1:160105602..160107369,2	K562	blood:
2	chr1:160099410..160101934-chr1:160112290..160114172,2	K562	blood:

Variant related genes	Relation type
ENSG00000018625	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1046995	0.92[ASN][1000 genomes]
rs10494336	0.95[ASN][1000 genomes]
rs1063125	0.87[ASN][1000 genomes]
rs10908761	0.85[ASN][1000 genomes]
rs16831388	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831438	0.91[ASN][1000 genomes]
rs16831441	0.89[ASN][1000 genomes]
rs17846707	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2070702	0.92[ASN][1000 genomes]
rs2070703	0.92[ASN][1000 genomes]
rs2070704	0.92[ASN][1000 genomes]
rs2753267	0.93[ASN][1000 genomes]
rs3747625	0.92[ASN][1000 genomes]
rs55967674	0.86[ASN][1000 genomes]
rs56199408	0.91[ASN][1000 genomes]
rs58313172	0.93[ASN][1000 genomes]
rs9660305	0.93[ASN][1000 genomes]
rs9661252	0.89[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	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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	esv3453724	chr1:160098374-160136495	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	esv3453725	chr1:160098456-160136351	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12136519	ATP1A4	cis	Muscle Skeletal	GTEx
rs12136519	ATP1A4	cis	Esophagus Muscularis	GTEx
rs12136519	ATP1A4	cis	Artery Tibial	GTEx
rs12136519	ATP1A4	cis	Adipose Subcutaneous	GTEx
rs12136519	ATP1A4	cis	Heart Left Ventricle	GTEx
rs12136519	ATP1A4	cis	Artery Aorta	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160088000-160146200	Weak transcription	Spleen	Spleen
2	chr1:160088800-160107400	Weak transcription	Fetal Brain Female	brain
3	chr1:160090200-160104600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:160090600-160112600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:160092400-160112200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:160093800-160101200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:160093800-160101800	Weak transcription	Gastric	stomach
8	chr1:160093800-160106600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:160094000-160112000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:160094800-160110200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:160095000-160103200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:160095400-160108200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:160097000-160101400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
14	chr1:160097000-160109800	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr1:160097200-160101400	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr1:160097200-160103400	Enhancers	Psoas Muscle	Psoas
17	chr1:160097200-160103400	Enhancers	Right Atrium	heart
18	chr1:160097200-160112200	Weak transcription	Brain Germinal Matrix	brain
19	chr1:160097400-160101400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:160097400-160101600	Weak transcription	Pancreas	Pancrea
21	chr1:160097400-160104800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:160097400-160107600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:160098000-160102600	Strong transcription	Rectal Smooth Muscle	rectum
24	chr1:160098200-160102000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:160098400-160103200	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:160098600-160112200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:160099000-160101400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:160099600-160101200	Enhancers	A549	lung
29	chr1:160099600-160102400	Enhancers	HepG2	liver
30	chr1:160099600-160107400	Weak transcription	Brain Angular Gyrus	brain
31	chr1:160099800-160104200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:160099800-160109000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:160100000-160102600	Enhancers	Adipose Nuclei	Adipose
34	chr1:160100000-160114800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:160100200-160101200	Enhancers	Brain Substantia Nigra	brain
36	chr1:160100200-160102200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:160100200-160102200	Genic enhancers	Stomach Smooth Muscle	stomach
38	chr1:160100200-160103000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:160100400-160101400	Enhancers	Lung	lung
40	chr1:160100400-160107200	Strong transcription	HSMMtube	muscle
41	chr1:160100600-160102000	Weak transcription	Aorta	Aorta
42	chr1:160100600-160105800	Weak transcription	Ovary	ovary
43	chr1:160100600-160112000	Strong transcription	Fetal Muscle Leg	muscle
44	chr1:160100800-160102000	Genic enhancers	Brain Anterior Caudate	brain
45	chr1:160100800-160102000	Weak transcription	Esophagus	oesophagus
46	chr1:160100800-160102800	Enhancers	Left Ventricle	heart
47	chr1:160100800-160104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:160100800-160104200	Weak transcription	Fetal Stomach	stomach
49	chr1:160100800-160105200	Weak transcription	HSMM	muscle
50	chr1:160101000-160101200	Enhancers	Brain Hippocampus Middle	brain

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