Variant report

Variant	rs902475
Chromosome Location	chr10:98882425-98882426
allele	A/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: 5 )

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

rs_ID	r²[population]
rs1336259	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1490689	0.86[EUR][1000 genomes]
rs1490690	0.87[EUR][1000 genomes]
rs1490691	0.96[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2006739	0.87[EUR][1000 genomes]
rs2484879	0.83[EUR][1000 genomes]
rs2636774	0.83[JPT][hapmap]
rs2636776	0.86[EUR][1000 genomes]
rs2636784	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2636786	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2636787	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2636813	0.82[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2636817	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2784938	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2817689	0.81[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2817691	0.89[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2817693	1.00[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs2817694	0.80[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2817701	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2817703	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2817704	0.80[EUR][1000 genomes]
rs2817705	0.83[EUR][1000 genomes]
rs2817709	0.83[EUR][1000 genomes]
rs2817710	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2817711	0.82[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2817713	0.83[JPT][hapmap];0.83[MEX][hapmap]
rs3000213	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs902469	0.83[JPT][hapmap]
rs902473	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs902474	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	0.86[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs902475	DHDPSL	cis	parietal	SCAN
rs902475	POLR2H	trans	cerebellum	SCAN
rs902475	C10orf131	cis	cerebellum	SCAN
rs902475	MORN4	cis	cerebellum	SCAN
rs902475	FRAT1	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	chr10:98882200-98882800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:98882400-98883400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:98882400-98883600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:98882400-98889400	Weak transcription	Brain Inferior Temporal Lobe	brain

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