Variant report

Variant	rs2299190
Chromosome Location	chr7:87577356-87577357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:87572122..87575217-chr7:87576874..87579518,3	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10235694	0.84[CEU][hapmap];0.95[MEX][hapmap]
rs10279744	0.95[MEX][hapmap]
rs10282572	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs11972409	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs12669586	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs12704380	0.88[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs12704381	0.82[AMR][1000 genomes]
rs1623535	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1629569	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs1631368	0.81[AMR][1000 genomes]
rs1637488	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs1637489	0.88[CEU][hapmap]
rs1637492	0.81[CEU][hapmap]
rs1637496	0.80[AMR][1000 genomes]
rs1637497	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs1637498	0.84[AMR][1000 genomes]
rs1637499	0.88[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs1637500	0.84[CEU][hapmap]
rs1637502	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1637503	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1637504	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1637505	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1637506	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1688886	0.88[CEU][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs1688887	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1688888	0.87[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1688890	0.88[CEU][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs1688891	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs1688893	0.80[AMR][1000 genomes]
rs1688894	0.82[AMR][1000 genomes]
rs1688895	0.80[AMR][1000 genomes]
rs1688898	0.81[AMR][1000 genomes]
rs1688899	0.88[CEU][hapmap]
rs1688901	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs1688902	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs17150161	0.84[CEU][hapmap]
rs2021741	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2022160	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2022163	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs2022555	0.84[CEU][hapmap]
rs2023533	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[MEX][hapmap]
rs2024019	0.80[CEU][hapmap]
rs2079422	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs2097917	0.83[CEU][hapmap]
rs2108087	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2158766	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs2282948	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs2282949	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap]
rs2282950	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs2373487	0.84[CEU][hapmap]
rs28794871	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6465124	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9641021	0.84[CEU][hapmap]

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	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023352	chr7:87418818-88192925	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539005	chr7:87418818-88192925	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv888696	chr7:87526944-87594188	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv525073	chr7:87535096-87812968	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299190	CDK14	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87565200-87580600	Weak transcription	Brain Anterior Caudate	brain
2	chr7:87565200-87582400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:87565200-87588000	Weak transcription	Fetal Brain Male	brain
4	chr7:87565800-87580600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:87568600-87578400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:87569200-87589600	Weak transcription	Fetal Lung	lung
7	chr7:87571400-87582400	Weak transcription	Dnd41	blood
8	chr7:87575400-87578400	Weak transcription	GM12878-XiMat	blood

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