Variant report

Variant	rs2553760
Chromosome Location	chr11:108753316-108753317
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	chr11:108745387..108747861-chr11:108753103..108755912,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10502103	0.85[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs10749925	0.85[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap]
rs12574567	0.85[CHB][hapmap]
rs12574721	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs12575278	0.81[CHB][hapmap]
rs12577382	0.80[ASN][1000 genomes]
rs12785398	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs12794048	0.84[CHB][hapmap]
rs12796331	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs12801974	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs12802313	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs12808060	0.85[CHB][hapmap]
rs12808674	0.82[CHD][hapmap]
rs1365046	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1365047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1365048	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108608	0.82[CHD][hapmap]
rs17108703	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs17108744	0.81[CHB][hapmap]
rs2042677	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2042678	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061681	0.85[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap]
rs2553749	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs2553750	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs2553751	0.85[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2553754	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]
rs2553757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553758	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615725	0.84[CEU][hapmap]
rs2615727	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs2615756	0.82[CEU][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2726885	0.87[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap]
rs2726886	0.85[CEU][hapmap];0.87[CHD][hapmap]
rs2726896	0.85[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs2726907	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726908	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726910	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726915	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34350110	0.80[ASN][1000 genomes]
rs34354308	0.80[ASN][1000 genomes]
rs35244070	0.80[ASN][1000 genomes]
rs35430545	0.81[ASN][1000 genomes]
rs4497371	0.85[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs57014838	0.82[ASN][1000 genomes]
rs71489925	0.80[ASN][1000 genomes]
rs898972	0.85[CHB][hapmap];0.82[CHD][hapmap];0.80[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
rs2553760	NPAT	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108726200-108768400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr11:108728400-108810600	Weak transcription	Left Ventricle	heart
3	chr11:108741800-108756600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:108742400-108753400	Weak transcription	Ovary	ovary
5	chr11:108744000-108754000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:108744800-108754800	Weak transcription	HSMM	muscle
7	chr11:108746400-108757000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:108750800-108756400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:108751600-108756600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:108752200-108755000	Weak transcription	HUVEC	blood vessel
11	chr11:108752200-108755400	Weak transcription	NH-A	brain
12	chr11:108752400-108757200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:108753200-108753400	Enhancers	GM12878-XiMat	blood
14	chr11:108753200-108754800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr11:108753200-108761000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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