Variant report

Variant	rs10890903
Chromosome Location	chr11:108749295-108749296
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:108723598..108725944-chr11:108749030..108751490,2	K562	blood:
2	chr11:108743296..108746092-chr11:108747045..108750308,3	K562	blood:
3	chr11:108746537..108749328-chr11:108750101..108751983,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10466523	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10502106	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10749923	0.83[EUR][1000 genomes]
rs10749926	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs10749927	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs10749928	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs10749929	0.96[CEU][hapmap];0.86[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10789675	0.84[EUR][1000 genomes]
rs10789676	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs10789677	0.83[EUR][1000 genomes]
rs10789678	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10789680	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10789681	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs10789682	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789683	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10789685	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10789688	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789691	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789693	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10789694	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10789696	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890877	0.84[EUR][1000 genomes]
rs10890879	0.84[EUR][1000 genomes]
rs10890883	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes]
rs10890888	0.84[EUR][1000 genomes]
rs10890889	0.89[EUR][1000 genomes]
rs10890893	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10890894	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890895	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10890897	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890898	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890899	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890901	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10890902	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10890905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890908	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11212750	0.84[EUR][1000 genomes]
rs11212771	0.96[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs11212774	0.85[EUR][1000 genomes]
rs11212797	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212802	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11212811	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11212816	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11212825	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11530525	0.84[EUR][1000 genomes]
rs12420572	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1824664	0.84[EUR][1000 genomes]
rs1824665	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1863366	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306118	0.84[EUR][1000 genomes]
rs2357224	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781864	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs3781866	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs3781867	0.83[EUR][1000 genomes]
rs3902843	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs4027488	0.85[EUR][1000 genomes]
rs4237580	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4497371	0.96[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4753849	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4753852	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4754354	0.85[EUR][1000 genomes]
rs4754357	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4754358	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4754359	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4754366	0.87[ASN][1000 genomes]
rs61912810	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7103086	0.85[EUR][1000 genomes]
rs7116062	0.84[EUR][1000 genomes]
rs7940595	0.84[EUR][1000 genomes]
rs890237	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs10890903	ZC3H12C	cis	parietal	SCAN

Chromatin state (count:14 , 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	chr11:108734600-108753200	Weak transcription	GM12878-XiMat	blood
4	chr11:108741800-108750400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:108741800-108756600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:108742400-108753400	Weak transcription	Ovary	ovary
7	chr11:108744000-108754000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:108744200-108751200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:108744800-108751200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:108744800-108754800	Weak transcription	HSMM	muscle
11	chr11:108745800-108751600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:108746200-108750800	Weak transcription	HUVEC	blood vessel
13	chr11:108746400-108757000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:108746600-108751800	Weak transcription	NH-A	brain

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