Variant report

Variant	rs2246616
Chromosome Location	chr21:40886816-40886817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11088478	0.95[ASN][1000 genomes]
rs11701190	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11701232	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11702769	0.99[ASN][1000 genomes]
rs12482418	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13046275	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13050145	0.95[ASN][1000 genomes]
rs13051411	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474384	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1475593	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1524929	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2009713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026268	0.96[ASN][1000 genomes]
rs2037668	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2178881	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2837043	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2837045	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2837046	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837047	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837048	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837049	0.99[ASN][1000 genomes]
rs2837050	0.99[ASN][1000 genomes]
rs2837051	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837052	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837053	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2837054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837055	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28634277	0.98[ASN][1000 genomes]
rs3787927	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4118060	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4816629	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818038	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818039	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818040	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818041	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4818042	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818044	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818045	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6517553	0.99[ASN][1000 genomes]
rs7277107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7278885	0.94[ASN][1000 genomes]
rs7280971	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7281076	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8126715	0.96[ASN][1000 genomes]
rs8126729	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8126860	0.99[ASN][1000 genomes]
rs8127748	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8128567	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8128795	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8131355	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8132867	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8132996	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8133292	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8133862	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9974333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9976202	0.99[ASN][1000 genomes]
rs9976208	0.81[CEU][hapmap];0.99[ASN][1000 genomes]
rs9983297	0.98[ASN][1000 genomes]
rs9983428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9984540	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2246616	LCA5L	cis	Nerve Tibial	GTEx
rs2246616	LCA5L	cis	Esophagus Mucosa	GTEx
rs2246616	LCA5L	cis	lung	GTEx
rs2246616	LCA5L	cis	Muscle Skeletal	GTEx
rs2246616	LCA5L	cis	Esophagus Muscularis	GTEx
rs2246616	LCA5L	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
2	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr21:40874800-40887000	Weak transcription	Aorta	Aorta
4	chr21:40875200-40890400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:40875400-40890200	Weak transcription	Brain Hippocampus Middle	brain
6	chr21:40875400-40890400	Weak transcription	Fetal Lung	lung
7	chr21:40875800-40895200	Weak transcription	Brain Substantia Nigra	brain
8	chr21:40875800-40898600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr21:40876400-40887600	Weak transcription	Left Ventricle	heart
10	chr21:40876400-40894600	Weak transcription	Gastric	stomach
11	chr21:40876400-40897400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr21:40877000-40891000	Weak transcription	Pancreas	Pancrea
13	chr21:40877200-40887000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr21:40877400-40899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr21:40878200-40889800	Weak transcription	Primary T cells from cord blood	blood
16	chr21:40880200-40899800	Weak transcription	Fetal Muscle Leg	muscle
17	chr21:40883200-40887800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr21:40883400-40890400	Weak transcription	Fetal Kidney	kidney
19	chr21:40884600-40887600	Weak transcription	Brain Anterior Caudate	brain
20	chr21:40885200-40888200	Enhancers	Fetal Brain Male	brain
21	chr21:40885400-40890600	Weak transcription	Fetal Heart	heart
22	chr21:40885600-40887600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr21:40885600-40891000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:40885800-40887800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr21:40886400-40888200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr21:40886800-40888200	Enhancers	Fetal Brain Female	brain

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