Variant report

Variant	rs2381203
Chromosome Location	chr2:142880602-142880603
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	chr2:142874759..142876508-chr2:142879340..142881781,2	MCF-7	breast:
2	chr2:142879155..142881671-chr2:142888554..142890515,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10190170	0.83[CHD][hapmap]
rs10193058	0.92[JPT][hapmap]
rs10496913	0.82[ASN][1000 genomes]
rs10496914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10803487	0.85[CHB][hapmap]
rs10928134	0.83[CHD][hapmap]
rs11680286	0.85[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs11688838	0.85[CHB][hapmap]
rs11691560	0.85[CHD][hapmap]
rs11691595	0.85[CHD][hapmap]
rs12472834	0.82[ASN][1000 genomes]
rs12621782	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs12988578	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13024219	0.85[ASN][1000 genomes]
rs13036224	0.85[CHB][hapmap]
rs1375609	0.85[CHD][hapmap]
rs1375611	0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs1375612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375613	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1375614	0.82[ASN][1000 genomes]
rs1449475	0.85[CHB][hapmap]
rs1449477	0.85[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs1449478	0.85[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1449480	0.85[CHD][hapmap]
rs1449482	0.85[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1449485	0.86[AFR][1000 genomes]
rs1449489	0.85[CHB][hapmap]
rs1449490	0.85[CHB][hapmap]
rs1449498	0.85[CHB][hapmap]
rs1449499	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs1449501	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs1449503	0.85[CHB][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs1449504	0.85[CHB][hapmap]
rs1868543	0.85[CHB][hapmap]
rs1868544	0.85[CHB][hapmap]
rs1900933	0.85[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap]
rs1900936	0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2029142	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs2060592	0.90[CHB][hapmap]
rs2218734	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs2290140	0.81[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs4662219	0.85[CHD][hapmap];0.91[MEX][hapmap]
rs4662370	0.83[CHD][hapmap]
rs4662373	0.85[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4662396	0.85[ASN][1000 genomes]
rs62155638	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707136	0.82[ASN][1000 genomes]
rs6744928	0.85[CHD][hapmap];0.91[MEX][hapmap]
rs6754907	0.85[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7558803	0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs7566250	0.88[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs7598886	0.83[CHB][hapmap]
rs7605112	0.85[CHB][hapmap]
rs7609479	0.85[CHD][hapmap]
rs957376	0.85[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs9941495	0.85[CHB][hapmap]
rs997123	0.86[AFR][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	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2381203	NXPH2	cis	cerebellum	SCAN
rs2381203	HNMT	cis	parietal	SCAN
rs2381203	ZEB2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142877800-142884000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:142878200-142886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:142878400-142883400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:142878800-142882400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:142879200-142887000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:142879400-142882400	Weak transcription	Brain Substantia Nigra	brain

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