Variant report

Variant	rs10896705
Chromosome Location	chr11:57909502-57909503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1031234	0.82[JPT][hapmap]
rs1031360	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs10750882	0.83[JPT][hapmap]
rs10750883	0.83[JPT][hapmap]
rs10750886	0.90[JPT][hapmap]
rs10750887	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10792135	0.82[JPT][hapmap]
rs10792139	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10896701	0.85[CHB][hapmap]
rs10896703	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896704	0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229240	0.82[LWK][hapmap]
rs11229247	0.83[JPT][hapmap]
rs11229250	0.83[JPT][hapmap]
rs11229273	0.82[JPT][hapmap]
rs12363350	0.83[JPT][hapmap]
rs1349482	0.82[JPT][hapmap]
rs1447165	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1447166	0.92[CEU][hapmap]
rs1447168	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs1447169	0.83[JPT][hapmap]
rs1451326	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap]
rs1900536	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs2044856	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2245676	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs2441970	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2443441	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2443447	0.88[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs2514176	0.92[CEU][hapmap]
rs3853677	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs3974323	0.83[JPT][hapmap]
rs4625485	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4939179	0.82[LWK][hapmap]
rs4939180	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs4939181	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4939182	0.83[JPT][hapmap]
rs6591455	0.83[JPT][hapmap]
rs7109726	0.83[JPT][hapmap]
rs7110748	0.82[JPT][hapmap]
rs7113347	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7117711	0.83[JPT][hapmap]
rs716945	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs895660	0.81[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv832166	chr11:57852031-58006189	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10896705	MS4A6A	cis	cerebellum	SCAN
rs10896705	TIMM10	cis	multi-tissue	Pritchard
rs10896705	SYT7	cis	cerebellum	SCAN
rs10896705	OR4C6	cis	parietal	SCAN
rs10896705	OR4D6	cis	cerebellum	SCAN
rs10896705	OR5AS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57909400-57909600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:57909400-57910400	Weak transcription	Fetal Lung	lung

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