Variant report

Variant	rs2964653
Chromosome Location	chr5:116028640-116028641
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	chr5:116016880..116019114-chr5:116028567..116031024,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10037986	0.94[ASN][1000 genomes]
rs10038005	0.93[ASN][1000 genomes]
rs10040214	0.93[ASN][1000 genomes]
rs10043155	0.99[ASN][1000 genomes]
rs1027291	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1027292	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1196	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1197	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12108958	0.83[ASN][1000 genomes]
rs12516894	0.93[ASN][1000 genomes]
rs17140312	0.94[ASN][1000 genomes]
rs17140330	0.99[ASN][1000 genomes]
rs2933593	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2933607	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2933608	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2933614	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2933616	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2933617	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2933627	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2933628	0.94[ASW][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.84[TSI][hapmap]
rs2933630	0.82[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs2933633	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2964648	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2964649	0.85[ASN][1000 genomes]
rs2964655	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964657	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964658	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964659	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964662	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964701	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2964702	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4512159	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4920860	0.93[ASN][1000 genomes]
rs4920925	0.95[ASN][1000 genomes]
rs4920926	0.98[ASN][1000 genomes]
rs4920927	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4920928	0.93[ASN][1000 genomes]
rs55946451	0.94[ASN][1000 genomes]
rs72663324	0.81[ASN][1000 genomes]
rs72663325	0.94[ASN][1000 genomes]
rs72663326	0.95[ASN][1000 genomes]
rs7701326	0.90[ASN][1000 genomes]
rs7711109	0.99[ASN][1000 genomes]
rs7728276	0.97[ASN][1000 genomes]
rs7728633	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763490	chr5:115918339-116138525	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv830456	chr5:115969066-116170718	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv527974	chr5:115987168-116303678	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv462403	chr5:115994775-116284378	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv599485	chr5:115994775-116284378	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1030056	chr5:116008971-116278725	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2964653	CCDC112	cis	parietal	SCAN
rs2964653	AP3S1	cis	cerebellum	SCAN
rs2964653	JPH3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116016000-116032000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:116022600-116031000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:116022800-116029600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:116022800-116031400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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