Variant report

Variant	rs2553754
Chromosome Location	chr11:108736146-108736147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108735096..108738037-chr11:108740814..108742369,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10502103	0.85[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs10749925	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap]
rs12574567	0.85[CHB][hapmap]
rs12574721	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12574758	0.82[ASN][1000 genomes]
rs12575278	0.81[CHB][hapmap]
rs12577382	0.82[ASN][1000 genomes]
rs12785398	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs12794048	0.84[CHB][hapmap]
rs12794597	0.81[ASN][1000 genomes]
rs12796331	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs12800516	0.85[CHB][hapmap]
rs12800726	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs12801974	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs12802313	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs12808060	0.85[CHB][hapmap]
rs12808674	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs1365046	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1365047	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1365048	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108608	0.85[CHD][hapmap]
rs17108703	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs17108744	0.81[CHB][hapmap]
rs2042677	1.00[ASN][1000 genomes]
rs2042678	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2061681	0.85[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap]
rs2553749	0.85[CHB][hapmap]
rs2553750	0.85[CHB][hapmap]
rs2553751	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2553757	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553758	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553760	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553761	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2615725	0.84[CEU][hapmap]
rs2615727	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs2615756	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs2726885	0.81[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap]
rs2726886	0.85[CEU][hapmap];0.84[CHD][hapmap]
rs2726896	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs2726907	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2726908	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2726910	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726911	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726913	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726915	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726916	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726920	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34350110	0.82[ASN][1000 genomes]
rs34354308	0.82[ASN][1000 genomes]
rs35244070	0.82[ASN][1000 genomes]
rs35430545	0.82[ASN][1000 genomes]
rs57014838	0.81[ASN][1000 genomes]
rs71489925	0.82[ASN][1000 genomes]
rs898972	0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs970162	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv898386	chr11:108409442-108831875	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv898389	chr11:108724639-108891986	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2553754	NPAT	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108707600-108740800	Weak transcription	HMEC	breast
2	chr11:108710200-108738200	Weak transcription	Gastric	stomach
3	chr11:108715400-108738200	Weak transcription	K562	blood
4	chr11:108721600-108742200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:108725000-108736600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:108725000-108737000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:108725000-108739600	Weak transcription	A549	lung
8	chr11:108725000-108740000	Weak transcription	NHDF-Ad	bronchial
9	chr11:108725000-108741000	Weak transcription	HSMMtube	muscle
10	chr11:108725000-108741400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:108725400-108737200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:108725400-108738400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:108725400-108740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:108725400-108740800	Weak transcription	NHEK	skin
15	chr11:108725400-108741000	Weak transcription	Brain Angular Gyrus	brain
16	chr11:108725800-108740000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:108726200-108740400	Weak transcription	Primary B cells from cord blood	blood
18	chr11:108726200-108768400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:108728400-108810600	Weak transcription	Left Ventricle	heart
20	chr11:108728600-108741000	Weak transcription	Primary T cells from cord blood	blood
21	chr11:108729800-108737200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:108730000-108737000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:108730000-108740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:108734600-108753200	Weak transcription	GM12878-XiMat	blood
25	chr11:108734800-108743600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:108735600-108736200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:108735600-108736400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:108735600-108736600	Enhancers	Osteobl	bone
29	chr11:108735800-108736400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:108735800-108736600	Enhancers	NH-A	brain
31	chr11:108735800-108741200	Weak transcription	Fetal Heart	heart
32	chr11:108736000-108741000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:108736000-108741800	Weak transcription	H1 Cell Line	embryonic stem cell

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