Variant report

Variant	rs6752606
Chromosome Location	chr2:179801042-179801043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10204089	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10930842	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs10930844	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12464521	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477346	0.82[CHB][hapmap]
rs13008198	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2366920	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35233376	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35444808	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36112235	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894069	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6731864	0.82[CHB][hapmap]
rs6747791	1.00[CHB][hapmap]
rs7564407	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875455	chr2:179732845-179909467	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv583756	chr2:179758007-179843612	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1000545	chr2:179768359-179843612	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv875456	chr2:179775893-179896787	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6752606	HOXD12	cis	cerebellum	SCAN
rs6752606	TTN	cis	parietal	SCAN
rs6752606	HOXD13	cis	cerebellum	SCAN
rs6752606	CCDC141	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179770000-179848200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:179775600-179824200	Weak transcription	Left Ventricle	heart
3	chr2:179775600-179826400	Weak transcription	Pancreas	Pancrea
4	chr2:179783000-179802400	Weak transcription	HSMMtube	muscle
5	chr2:179784000-179802200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:179794600-179822800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:179796000-179802200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:179797000-179801800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:179800400-179804000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:179801000-179801400	ZNF genes & repeats	Primary B cells from cord blood	blood

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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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