Variant report

Variant	rs2406254
Chromosome Location	chr12:87092666-87092667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10431400	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10745430	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs10776992	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10776999	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10858436	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs10858444	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs10858463	0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10858465	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10858468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1159292	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1469383	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1560015	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1560016	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1981947	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1987803	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2013257	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs2114893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2162673	0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs2162674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2195231	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2406250	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406252	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2559814	0.83[JPT][hapmap]
rs2702774	0.83[JPT][hapmap]
rs2702775	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs4240751	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4399378	0.91[CEU][hapmap]
rs4454789	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4465427	0.81[ASN][1000 genomes]
rs4842819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4842820	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6538046	0.89[CHB][hapmap];0.92[CHD][hapmap]
rs717681	0.81[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7297574	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs7314362	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7314413	0.81[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7968485	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973223	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs7977253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981142	0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap]
rs982037	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs994288	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv899395	chr12:86813367-87177972	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916862	chr12:86837694-87718558	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv899396	chr12:86863041-87276957	ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv899397	chr12:86863041-87636831	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv899399	chr12:86880442-87177972	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv916604	chr12:86966256-87275268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1049580	chr12:86966497-87354132	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv899400	chr12:87055983-87194443	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1050699	chr12:87061020-87137487	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv455681	chr12:87064588-87132840	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv559691	chr12:87064588-87132840	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2406254	KITLG	cis	cerebellum	SCAN
rs2406254	NFKB2	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:87091400-87093000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:87091600-87093400	Enhancers	NHDF-Ad	bronchial
3	chr12:87092000-87092800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:87092000-87093400	Enhancers	Fetal Brain Male	brain
5	chr12:87092200-87092800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:87092200-87092800	Enhancers	Adipose Nuclei	Adipose
7	chr12:87092200-87092800	Flanking Active TSS	Osteobl	bone
8	chr12:87092400-87092800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr12:87092600-87092800	Enhancers	HSMMtube	muscle
10	chr12:87092600-87093000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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