Variant report

Variant	rs902474
Chromosome Location	chr10:98882374-98882375
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98874182..98876788-chr10:98880678..98883082,2	K562	blood:
2	chr10:98876065..98877734-chr10:98879477..98883103,3	K562	blood:
3	chr10:98880505..98883448-chr10:98886169..98887712,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1336259	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490689	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1490690	0.83[EUR][1000 genomes]
rs1490691	0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2006739	0.83[EUR][1000 genomes]
rs2484879	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2636776	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2636784	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636786	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636787	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2636813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2636817	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2784938	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2817647	0.87[YRI][hapmap]
rs2817689	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2817690	0.89[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes]
rs2817691	0.80[MEX][hapmap]
rs2817693	0.88[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2817694	0.96[CEU][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2817701	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817703	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817704	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817705	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817707	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817709	0.84[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817711	0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs2817713	0.88[MEX][hapmap];0.88[YRI][hapmap]
rs3000213	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs902473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902475	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs931451	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2758236	chr10:98789963-98962472	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2759777	chr10:98789963-98962472	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv895913	chr10:98854410-98884402	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs902474	CWF19L1	cis	cerebellum	SCAN
rs902474	CWF19L1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98870200-98887800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:98873600-98890000	Strong transcription	Fetal Thymus	thymus
3	chr10:98878800-98883000	Enhancers	Fetal Brain Male	brain
4	chr10:98879600-98883000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:98879600-98887600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:98880200-98912800	Weak transcription	Thymus	Thymus
7	chr10:98880400-98891600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:98881800-98883600	Weak transcription	Brain Germinal Matrix	brain
9	chr10:98882000-98884200	Weak transcription	Fetal Brain Female	brain
10	chr10:98882200-98882400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:98882200-98882400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:98882200-98882400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr10:98882200-98882800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain

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