Variant report

Variant	rs2171143
Chromosome Location	chr3:85084508-85084509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12714616	0.92[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12714617	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13066623	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13075494	0.80[AMR][1000 genomes]
rs13078384	1.00[CHB][hapmap]
rs13082518	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13092125	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13095644	1.00[CHB][hapmap]
rs13096651	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101344	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4516626	1.00[CHB][hapmap]
rs4856554	0.84[TSI][hapmap]
rs6791363	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs6808586	1.00[CHB][hapmap]
rs7628129	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7630382	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9309967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9647393	0.92[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9815258	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs9818659	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs9821807	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9823454	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs9828496	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9835904	1.00[CHB][hapmap]
rs9838091	1.00[CHB][hapmap]
rs9860513	0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs9870384	0.82[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs9873321	1.00[CHB][hapmap]
rs9874302	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9876378	0.89[ASN][1000 genomes]
rs9877460	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9878472	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9878707	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9881257	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs9883443	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

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	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2171143	CADM2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85068600-85090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85079600-85086400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:85081400-85088800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:85082200-85086400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:85082200-85088800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:85082600-85090000	Weak transcription	Fetal Brain Female	brain
7	chr3:85082600-85090400	Weak transcription	Fetal Brain Male	brain
8	chr3:85082600-85091600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:85083000-85090800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:85083200-85088800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:85083600-85088800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:85083800-85089000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:85083800-85089200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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