Variant report

Variant	rs12305552
Chromosome Location	chr12:41797386-41797387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10161143	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11180887	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs11180888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11180898	0.87[EUR][1000 genomes]
rs11180905	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11180907	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11180908	0.91[EUR][1000 genomes]
rs11180912	1.00[CEU][hapmap]
rs11180914	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12296173	0.91[EUR][1000 genomes]
rs12298553	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12299762	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12300549	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12305318	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12307517	0.93[ASN][1000 genomes]
rs12308926	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12312032	1.00[CEU][hapmap]
rs12314242	0.91[ASN][1000 genomes]
rs12314805	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs12318761	0.91[EUR][1000 genomes]
rs12321550	0.91[EUR][1000 genomes]
rs12322196	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1350433	0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1458155	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1534277	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs17129267	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17129287	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17129295	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17129296	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17129305	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17129347	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs17129351	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17129364	0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17129405	0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17129413	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1817270	0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2405924	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs285585	1.00[CEU][hapmap]
rs2897270	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3761676	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4558215	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs58573939	0.93[ASN][1000 genomes]
rs59662716	0.93[ASN][1000 genomes]
rs60903037	0.89[ASN][1000 genomes]
rs7133340	0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7297699	0.88[ASN][1000 genomes]
rs7305541	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs73274484	0.99[ASN][1000 genomes]
rs73278055	0.80[ASN][1000 genomes]
rs74077585	0.99[ASN][1000 genomes]
rs74077591	0.93[ASN][1000 genomes]
rs74077600	0.96[EUR][1000 genomes]
rs74078808	0.96[EUR][1000 genomes]
rs74078810	0.87[EUR][1000 genomes]
rs74078819	0.96[EUR][1000 genomes]
rs987823	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832383	chr12:41693298-41846934	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv899036	chr12:41777144-41807859	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv899037	chr12:41777144-41819215	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv1044910	chr12:41778831-41813198	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
6	esv2761735	chr12:41780758-41811938	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
7	esv2757501	chr12:41780758-41816002	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv2759896	chr12:41780758-41816002	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
9	esv2755020	chr12:41780758-41820936	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
10	nsv899038	chr12:41784137-41819215	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
11	nsv818915	chr12:41784997-41811063	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
12	nsv899039	chr12:41784997-41813207	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
13	nsv1050627	chr12:41789891-41809009	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
14	esv3338595	chr12:41794910-41797658	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	n/a
15	esv3322787	chr12:41795085-41797483	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12305552	TTR	trans	brain	seeQTL
rs12305552	GUCA1C	trans	brain	seeQTL
rs12305552	LRTM1	trans	brain	seeQTL
rs12305552	NKAP	trans	brain	seeQTL
rs12305552	SH2D2A	trans	brain	seeQTL
rs12305552	SLC5A7	trans	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41796600-41797800	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr12:41796800-41797800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr12:41797000-41797600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr12:41797000-41797800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr12:41797000-41798000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:41797000-41798400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:41797000-41800600	Weak transcription	Brain Anterior Caudate	brain
8	chr12:41797200-41797800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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