Variant report

Variant	rs12828347
Chromosome Location	chr12:31925493-31925494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12811651	1.00[AFR][1000 genomes]
rs12816956	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12817263	0.88[CEU][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes]
rs12825723	0.88[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap]
rs17566133	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17566497	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17568410	0.85[MEX][hapmap]
rs34044630	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34065684	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34121037	1.00[AFR][1000 genomes]
rs34184907	1.00[AFR][1000 genomes]
rs34353434	1.00[AFR][1000 genomes]
rs34777422	1.00[AFR][1000 genomes]
rs35774037	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36058687	0.88[EUR][1000 genomes]
rs4930990	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930991	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930993	1.00[AFR][1000 genomes]
rs4931527	1.00[ASN][1000 genomes]
rs4931556	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931569	1.00[AFR][1000 genomes]
rs4931573	0.88[CEU][hapmap]
rs4931574	1.00[AFR][1000 genomes]
rs4931576	0.85[MEX][hapmap]
rs55924094	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61736289	1.00[ASN][1000 genomes]
rs61932066	1.00[AFR][1000 genomes]
rs66550728	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7977983	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	nsv558101	chr12:31876666-32006563	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv1050448	chr12:31877289-31927006	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv8940	chr12:31899904-31987363	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12828347	REP15	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31913200-31926200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:31921200-31925800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:31921200-31926200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:31921400-31925800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:31921400-31925800	Weak transcription	Fetal Thymus	thymus
6	chr12:31921400-31926400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:31925000-31927800	Enhancers	HepG2	liver
8	chr12:31925200-31927000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:31925400-31925800	Enhancers	Liver	Liver
10	chr12:31925400-31926400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:31925400-31926400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr12:31925400-31926600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr12:31925400-31926600	Enhancers	Gastric	stomach
14	chr12:31925400-31927200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:31925400-31927200	Enhancers	Pancreas	Pancrea
16	chr12:31925400-31927200	Enhancers	Stomach Mucosa	stomach
17	chr12:31925400-31927400	Enhancers	A549	lung

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