Variant report

Variant	rs2378603
Chromosome Location	chr1:222939905-222939906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12043288	0.89[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12749296	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17532708	0.89[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2068814	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2378607	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28521319	0.90[EUR][1000 genomes]
rs28654270	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28765200	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28787398	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34885880	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35300015	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35725247	0.86[EUR][1000 genomes]
rs35806535	0.94[CHD][hapmap]
rs4282830	0.86[EUR][1000 genomes]
rs61824331	0.87[EUR][1000 genomes]
rs61825253	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61825254	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61825255	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61825258	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61825259	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6683071	0.90[CHD][hapmap]
rs6700083	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv3369664	chr1:222935606-222958164	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2378603	HHIPL2	cis	cerebellum	SCAN
rs2378603	TGFB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222934800-222940000	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:222939400-222941400	Enhancers	Dnd41	blood
3	chr1:222939600-222940000	ZNF genes & repeats	Primary B cells from cord blood	blood
4	chr1:222939800-222941000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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