Variant report

Variant	rs12706740
Chromosome Location	chr7:126296428-126296429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10255379	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1361986	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs2237761	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299493	0.91[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2402820	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3824014	0.88[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs4731320	0.91[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6954055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6975231	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7792723	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7803165	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7804379	0.82[JPT][hapmap]
rs7808017	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs8180790	0.90[ASN][1000 genomes]
rs9691497	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]

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	nsv529300	chr7:125669493-126587858	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1032938	chr7:126067684-126587859	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv539119	chr7:126067684-126587859	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv889187	chr7:126219766-126478190	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1032108	chr7:126278349-126362592	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv5939	chr7:126279355-126322778	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12706740	TMEM229A	cis	cerebellum	SCAN
rs12706740	TAGLN	trans	brain	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126295800-126296600	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr7:126296000-126296800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr7:126296200-126296600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:126296200-126297000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr7:126296400-126299400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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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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