Variant report

Variant	rs2897092
Chromosome Location	chr12:86038330-86038331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10083104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10466964	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779165	0.88[ASN][1000 genomes]
rs10779166	0.88[ASN][1000 genomes]
rs10779174	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779179	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779180	0.85[EUR][1000 genomes]
rs10779181	0.86[EUR][1000 genomes]
rs10779182	0.86[EUR][1000 genomes]
rs10779188	0.82[EUR][1000 genomes]
rs10862989	0.80[GIH][hapmap]
rs10862992	0.81[ASN][1000 genomes]
rs10862994	0.88[ASN][1000 genomes]
rs10862995	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10862997	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10862998	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863006	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863019	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10863021	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10863022	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863023	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863032	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10863034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863035	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863039	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863045	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11116857	0.81[ASN][1000 genomes]
rs11116913	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11116933	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11116934	0.85[EUR][1000 genomes]
rs11116935	0.85[EUR][1000 genomes]
rs11116945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11116947	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11116964	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11116965	0.82[EUR][1000 genomes]
rs11116966	0.82[EUR][1000 genomes]
rs11116967	0.82[EUR][1000 genomes]
rs11116968	0.82[EUR][1000 genomes]
rs11116969	0.82[EUR][1000 genomes]
rs11116971	0.93[ASN][1000 genomes]
rs11835161	0.80[EUR][1000 genomes]
rs12230791	0.81[ASN][1000 genomes]
rs12303708	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12308693	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12311475	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12318024	0.88[ASN][1000 genomes]
rs12578708	0.84[EUR][1000 genomes]
rs17013043	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1870936	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2199506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2199508	0.86[EUR][1000 genomes]
rs2199510	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2199511	0.85[EUR][1000 genomes]
rs2199512	0.85[EUR][1000 genomes]
rs2199513	0.84[EUR][1000 genomes]
rs2199515	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2219710	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2219711	0.84[EUR][1000 genomes]
rs2405254	0.85[EUR][1000 genomes]
rs2405256	0.86[EUR][1000 genomes]
rs2405257	0.85[EUR][1000 genomes]
rs2405260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637596	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34750736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4143506	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897817	0.85[EUR][1000 genomes]
rs4897825	0.85[EUR][1000 genomes]
rs4897842	0.82[EUR][1000 genomes]
rs4897843	0.82[EUR][1000 genomes]
rs6539898	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539902	0.85[EUR][1000 genomes]
rs67352195	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7133064	0.85[EUR][1000 genomes]
rs7295445	0.83[EUR][1000 genomes]
rs7300819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302629	0.85[EUR][1000 genomes]
rs7304475	0.86[EUR][1000 genomes]
rs7308482	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310496	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7316167	0.85[EUR][1000 genomes]
rs7397867	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7485843	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7488757	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7955601	0.85[EUR][1000 genomes]
rs7966898	0.86[EUR][1000 genomes]
rs7973153	0.85[EUR][1000 genomes]
rs7975674	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976228	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817242	chr12:85622245-86069213	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751125	chr12:85884858-86098240	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1043253	chr12:85888151-86125364	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1037938	chr12:85902517-86045125	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2761758	chr12:85906092-86045137	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv559665	chr12:85908396-86070692	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2751126	chr12:85912432-86061403	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1052187	chr12:85954455-86278200	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv541560	chr12:85954455-86278200	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1054475	chr12:85985510-86175711	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv541561	chr12:85985510-86175711	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv430522	chr12:86010755-86069542	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1042467	chr12:86017619-86078149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv522439	chr12:86020998-86066266	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2897092	NTS	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86037000-86038400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:86037000-86040000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:86037000-86042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:86038200-86038800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:86038200-86040400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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