Variant report

Variant	rs939664
Chromosome Location	chr2:213038087-213038088
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213032041..213033643-chr2:213036583..213039398,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12694265	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13029563	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13030421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13035998	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs1357140	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs1402765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1402766	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1521648	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1521653	0.88[JPT][hapmap]
rs2103002	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2371477	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4527160	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs62182564	0.90[AFR][1000 genomes]
rs6736654	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741280	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6751662	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752323	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7591480	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7594859	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs939223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011572	chr2:212840066-213152279	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv875805	chr2:212891401-213164837	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875806	chr2:212997024-213211067	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs939664	HIP1R	trans	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213037800-213039400	Enhancers	HUVEC	blood vessel
2	chr2:213037800-213041200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:213038000-213038200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:213038000-213038800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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