Variant report

Variant	rs2636788
Chromosome Location	chr10:98876941-98876942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12782356	0.88[CEU][hapmap]
rs17112401	0.82[CEU][hapmap]
rs2451766	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2636777	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2636781	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2636782	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs2636783	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs2636785	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2636789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2636814	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2636815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2636816	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817692	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2817695	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817696	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2817697	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817698	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs2817702	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2636788	MRPL43	cis	parietal	SCAN
rs2636788	C10orf129	cis	cerebellum	SCAN
rs2636788	C10orf131	cis	cerebellum	SCAN
rs2636788	DHDPSL	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98870200-98879800	Weak transcription	Thymus	Thymus
2	chr10:98870200-98887800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:98872200-98877800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr10:98873600-98890000	Strong transcription	Fetal Thymus	thymus
5	chr10:98875800-98877000	Enhancers	Fetal Brain Male	brain
6	chr10:98875800-98877200	Enhancers	Fetal Brain Female	brain
7	chr10:98876600-98878800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:98876600-98879200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:98876800-98877600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr10:98876800-98878000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:98876800-98879000	Weak transcription	Brain Germinal Matrix	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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