Variant report

Variant	rs12883863
Chromosome Location	chr14:37630699-37630700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10135285	0.83[TSI][hapmap]
rs10136755	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs10137539	1.00[JPT][hapmap]
rs10139726	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10140136	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10150704	0.83[TSI][hapmap]
rs10483486	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1080374	0.81[EUR][1000 genomes]
rs11156934	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs11620965	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs11848427	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12879089	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879259	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12883655	0.81[EUR][1000 genomes]
rs12883794	0.81[EUR][1000 genomes]
rs12889779	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12893236	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12897101	1.00[JPT][hapmap]
rs12897482	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106164	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs17554224	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1950526	0.86[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap]
rs2093119	0.83[TSI][hapmap]
rs2899854	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34164918	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503846	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35127962	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35130743	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35281444	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322850	0.80[CEU][hapmap];0.86[TSI][hapmap]
rs35412613	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35424693	1.00[ASN][1000 genomes]
rs35799924	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36057482	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36112910	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4344641	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4368077	1.00[ASN][1000 genomes]
rs4522325	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988260	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61988264	0.81[EUR][1000 genomes]
rs61988282	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61988284	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988286	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988287	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988312	0.85[ASN][1000 genomes]
rs61988340	0.82[ASN][1000 genomes]
rs6571776	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs6571777	1.00[JPT][hapmap]
rs6571791	0.81[EUR][1000 genomes]
rs6571792	0.80[EUR][1000 genomes]
rs6571794	0.80[EUR][1000 genomes]
rs714229	0.83[TSI][hapmap]
rs714230	0.83[TSI][hapmap]
rs7142673	0.83[TSI][hapmap]
rs7143414	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7143703	0.81[EUR][1000 genomes]
rs7143872	0.80[CEU][hapmap];0.86[TSI][hapmap]
rs7143938	0.86[TSI][hapmap]
rs7145475	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145768	0.80[CEU][hapmap]
rs7149154	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7149939	0.86[TSI][hapmap]
rs7151191	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs7151497	0.83[TSI][hapmap]
rs7153180	0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs7157361	0.81[EUR][1000 genomes]
rs7359156	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs8006144	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8007653	0.85[ASN][1000 genomes]
rs8008894	1.00[JPT][hapmap]
rs8012018	0.83[TSI][hapmap]
rs8014303	0.81[EUR][1000 genomes]
rs8015843	0.80[EUR][1000 genomes]
rs8015845	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs8016262	0.80[EUR][1000 genomes]
rs8016558	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8016567	1.00[JPT][hapmap]
rs8018493	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8018823	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs8019549	0.83[TSI][hapmap]
rs8019652	1.00[ASN][1000 genomes]
rs8021181	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022156	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910509	0.83[TSI][hapmap]
rs9989229	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534288	chr14:37254539-37697745	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1050174	chr14:37556357-37664143	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1043410	chr14:37556357-37671059	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv915783	chr14:37607836-38002966	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1036854	chr14:37609535-38013533	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak 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	16 gene(s)	inside rSNPs	diseases
7	nsv542045	chr14:37609535-38013533	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv901635	chr14:37623177-37782273	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12883863	SIP1	cis	cerebellum	SCAN
rs12883863	SEC23A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:37630000-37638000	Weak transcription	Pancreas	Pancrea

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