Variant report

Variant	rs12473127
Chromosome Location	chr2:183726031-183726032
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10182016	0.85[ASN][1000 genomes]
rs10202627	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10803961	0.99[ASN][1000 genomes]
rs10931042	0.87[ASN][1000 genomes]
rs10931044	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10931045	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931046	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931049	0.92[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11686953	0.87[ASN][1000 genomes]
rs11900716	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12466685	0.84[ASN][1000 genomes]
rs12469777	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12476544	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12476897	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611837	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693326	0.80[ASN][1000 genomes]
rs12990735	0.88[ASN][1000 genomes]
rs12992123	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13015615	0.81[ASN][1000 genomes]
rs13026760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1584734	1.00[ASN][1000 genomes]
rs2100344	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118590	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs21714	0.97[ASN][1000 genomes]
rs2242070	0.87[ASN][1000 genomes]
rs288247	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288248	0.97[ASN][1000 genomes]
rs288249	0.96[ASN][1000 genomes]
rs288330	0.92[ASN][1000 genomes]
rs2887227	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34528848	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs409238	0.99[ASN][1000 genomes]
rs4293535	0.93[ASN][1000 genomes]
rs430350	1.00[ASN][1000 genomes]
rs4311031	0.86[ASN][1000 genomes]
rs4338928	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581857	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4666867	0.85[ASN][1000 genomes]
rs55899538	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59146529	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433991	1.00[ASN][1000 genomes]
rs6433992	0.99[ASN][1000 genomes]
rs6433994	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs722738	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74178517	0.85[ASN][1000 genomes]
rs7560782	0.87[ASN][1000 genomes]
rs7562344	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7564919	0.86[ASN][1000 genomes]
rs7605198	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs825529	0.89[ASN][1000 genomes]
rs9973404	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2756954	chr2:183528670-183764930	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv34847	chr2:183537399-183786763	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
6	nsv1006265	chr2:183666013-183777604	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv536071	chr2:183666013-183777604	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv818096	chr2:183701588-183827018	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv875484	chr2:183702964-183747442	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12473127	NUP35	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183719600-183727000	Weak transcription	Aorta	Aorta
2	chr2:183719600-183727000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:183719600-183730800	Weak transcription	Psoas Muscle	Psoas
4	chr2:183722200-183730800	Weak transcription	Placenta	Placenta
5	chr2:183722400-183726600	Weak transcription	Fetal Stomach	stomach
6	chr2:183722400-183726800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:183723800-183730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:183724200-183730800	Weak transcription	Right Atrium	heart
9	chr2:183725200-183726400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:183725400-183726600	Weak transcription	Liver	Liver
11	chr2:183725800-183726200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:183725800-183726200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:183726000-183726200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:183726000-183726200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr2:183726000-183726600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:183726000-183727000	Enhancers	Colon Smooth Muscle	Colon
17	chr2:183726000-183730800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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