Variant report

Variant	rs2175276
Chromosome Location	chr11:57739207-57739208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1031232	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs11822108	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11824895	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12417338	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12418614	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12419427	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12419849	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs12420385	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs12421556	0.86[ASN][1000 genomes]
rs1349483	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1447182	0.90[CEU][hapmap]
rs17458061	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17538527	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs2441964	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs2866831	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41325844	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs55665208	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55920028	0.96[EUR][1000 genomes]
rs56023680	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56054495	0.93[EUR][1000 genomes]
rs56245847	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61903961	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61903969	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61904010	0.86[ASN][1000 genomes]
rs61904013	0.86[ASN][1000 genomes]
rs61904025	0.86[ASN][1000 genomes]
rs61905316	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905341	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905342	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905343	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905344	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905345	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107162	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs7108167	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112942	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7121825	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7128781	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72915744	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72917859	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72919837	0.86[ASN][1000 genomes]
rs7925491	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942438	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7944888	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7945120	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs921443	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv517822	chr11:57728993-57751001	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2175276	MS4A7	cis	cerebellum	SCAN
rs2175276	OR5L2	cis	parietal	SCAN
rs2175276	YPEL4	cis	multi-tissue	Pritchard
rs2175276	MS4A6A	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57735800-57739800	Enhancers	HepG2	liver
2	chr11:57738800-57740200	Weak transcription	Pancreas	Pancrea
3	chr11:57738800-57740400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:57738800-57745200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:57739000-57742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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