Variant report

Variant	rs12760321
Chromosome Location	chr1:213083261-213083262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10746436	0.85[GIH][hapmap]
rs10779596	0.98[ASN][1000 genomes]
rs10864024	0.93[ASN][1000 genomes]
rs10864030	0.98[ASN][1000 genomes]
rs11120063	0.91[ASN][1000 genomes]
rs11586329	0.95[AFR][1000 genomes]
rs12038555	0.95[ASN][1000 genomes]
rs12040492	0.95[ASN][1000 genomes]
rs12074192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs12075289	0.91[ASN][1000 genomes]
rs12087017	0.90[AFR][1000 genomes]
rs12087098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12135746	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12405742	0.86[ASN][1000 genomes]
rs12408694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12735579	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1284851	0.91[ASN][1000 genomes]
rs1284853	0.91[ASN][1000 genomes]
rs1390501	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs15903	0.91[ASN][1000 genomes]
rs2359323	0.98[ASN][1000 genomes]
rs2359326	0.93[ASN][1000 genomes]
rs2644549	0.95[ASN][1000 genomes]
rs2792562	0.95[ASN][1000 genomes]
rs28826102	0.96[AFR][1000 genomes]
rs28886307	0.94[AFR][1000 genomes]
rs4951473	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4951650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951651	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951652	0.88[AFR][1000 genomes]
rs58128459	0.91[ASN][1000 genomes]
rs6660933	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6663568	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6663574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671740	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674782	0.81[ASN][1000 genomes]
rs6679775	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6682947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6683314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs6697099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697126	0.91[ASN][1000 genomes]
rs6701782	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530057	0.87[ASN][1000 genomes]
rs7553536	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9429894	0.91[ASN][1000 genomes]
rs9429895	0.91[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	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1007129	chr1:213037244-213083261	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3403224	chr1:213081429-213085627	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3437401	chr1:213082329-213088502	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3337955	chr1:213083029-213088127	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3428295	chr1:213083029-213088127	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12760321	LOC642946	cis	multi-tissue	Pritchard
rs12760321	C1orf48	cis	multi-tissue	Pritchard
rs12760321	NSL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213073800-213089000	Weak transcription	Pancreas	Pancrea
2	chr1:213076800-213083600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:213079600-213090000	Weak transcription	Right Atrium	heart
4	chr1:213081600-213088000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:213082600-213083600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:213083000-213083400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:213083000-213083400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:213083200-213083400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:213083200-213084200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:213083200-213084200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:213083200-213084200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:213083200-213084200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:213083200-213084200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:213083200-213084600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:213083200-213086400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:213083200-213088000	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:213083200-213089000	Active TSS	H9 Cell Line	embryonic stem cell

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