Variant report

Variant	rs2058415
Chromosome Location	chr7:117770679-117770680
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10228816	0.81[EUR][1000 genomes]
rs10254348	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10258010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10269710	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12540880	0.85[CEU][hapmap]
rs17141135	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3808175	0.86[GIH][hapmap]
rs3808178	0.86[GIH][hapmap]
rs4141027	0.85[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4727861	0.90[EUR][1000 genomes]
rs4730826	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62468162	0.90[EUR][1000 genomes]
rs62468163	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6964881	0.86[GIH][hapmap]
rs6979426	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7792264	0.86[GIH][hapmap]
rs7792296	0.86[GIH][hapmap]
rs7796775	0.86[GIH][hapmap]
rs7798529	0.86[GIH][hapmap]
rs7804943	0.86[JPT][hapmap]
rs7805538	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs7809742	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs7811055	0.86[GIH][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2752146	chr7:117739049-117792049	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1016264	chr7:117739146-117792988	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2761358	chr7:117739158-117793000	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv608260	chr7:117739400-117792838	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1028064	chr7:117740164-117792988	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	esv3428352	chr7:117754050-117783524	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv33380	chr7:117768471-117793477	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2058415	TSPAN12	cis	parietal	SCAN
rs2058415	KCND2	cis	parietal	SCAN
rs2058415	TFEC	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117768800-117773400	Weak transcription	Fetal Brain Male	brain
2	chr7:117769400-117773000	Weak transcription	Fetal Brain Female	brain
3	chr7:117770400-117771200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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