Variant report

Variant	rs1542
Chromosome Location	chr3:178739594-178739595
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	chr3:178737773..178739885-chr3:179056978..179059649,2	K562	blood:
2	chr3:178733361..178735780-chr3:178739021..178740577,2	K562	blood:

Variant related genes	Relation type
ENSG00000260743	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs4325967	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4469018	0.83[ASN][1000 genomes]
rs4579062	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4607155	0.83[ASN][1000 genomes]
rs4632588	0.80[ASN][1000 genomes]
rs4637331	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4955807	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4955810	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6772028	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6790867	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6793893	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6794956	0.83[ASN][1000 genomes]
rs6795238	0.83[ASN][1000 genomes]
rs6800015	0.82[JPT][hapmap]
rs6804084	0.82[JPT][hapmap]
rs7639391	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9831543	1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9835765	0.83[ASN][1000 genomes]
rs9860318	0.80[ASN][1000 genomes]
rs9860749	0.80[ASN][1000 genomes]
rs9878734	0.80[ASN][1000 genomes]
rs9880749	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1009143	chr3:178731525-178783915	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv1799481	chr3:178733212-178782021	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1542	ATP11B	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178716400-178755000	Weak transcription	Pancreas	Pancrea
2	chr3:178717400-178744400	Weak transcription	HMEC	breast
3	chr3:178722200-178751600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:178723400-178749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:178723800-178754200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:178731400-178744400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:178732600-178744200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:178733400-178751400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:178733800-178742000	Weak transcription	Liver	Liver
10	chr3:178733800-178754600	Weak transcription	Lung	lung
11	chr3:178734000-178755200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:178734000-178755400	Weak transcription	HepG2	liver
13	chr3:178735000-178742200	Weak transcription	NHDF-Ad	bronchial
14	chr3:178735000-178742800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:178735000-178742800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:178735000-178763800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:178735600-178744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:178735600-178745600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:178735800-178751600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:178736000-178741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:178736200-178744400	Weak transcription	NHLF	lung
22	chr3:178737400-178739800	Genic enhancers	GM12878-XiMat	blood
23	chr3:178737600-178739600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:178737600-178739600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr3:178737600-178739800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:178737600-178740000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:178737600-178740000	Enhancers	HUVEC	blood vessel
28	chr3:178737600-178740200	Genic enhancers	HSMMtube	muscle
29	chr3:178737800-178739800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr3:178737800-178739800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:178738000-178739600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:178738000-178739800	Enhancers	K562	blood
33	chr3:178738000-178740000	Genic enhancers	HSMM	muscle
34	chr3:178738000-178764000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:178738200-178740200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:178738200-178744400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:178738200-178751600	Weak transcription	Stomach Mucosa	stomach
38	chr3:178738400-178739800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:178738400-178740200	Enhancers	Dnd41	blood
40	chr3:178738400-178745000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:178738600-178739800	Strong transcription	NH-A	brain
42	chr3:178738600-178740400	Weak transcription	Primary B cells from cord blood	blood
43	chr3:178738600-178742200	Weak transcription	Fetal Thymus	thymus
44	chr3:178738600-178744400	Weak transcription	Fetal Lung	lung
45	chr3:178738600-178744400	Weak transcription	Small Intestine	intestine
46	chr3:178738600-178745200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:178738600-178745600	Weak transcription	Brain Anterior Caudate	brain
48	chr3:178738600-178745600	Weak transcription	Thymus	Thymus
49	chr3:178738600-178748400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:178738600-178751600	Weak transcription	Adipose Nuclei	Adipose

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