Variant report

Variant	rs9983428
Chromosome Location	chr21:40875174-40875175
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40870583..40873437-chr21:40873635..40876593,2	K562	blood:
2	chr21:40873636..40875613-chr21:40877130..40879236,2	K562	blood:
3	chr21:40868881..40871731-chr21:40873960..40875993,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185437	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11088478	0.96[ASN][1000 genomes]
rs11701190	0.98[ASN][1000 genomes]
rs11701232	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11702769	1.00[ASN][1000 genomes]
rs12482418	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13046275	0.83[CEU][hapmap];0.95[ASN][1000 genomes]
rs13050145	0.96[ASN][1000 genomes]
rs13051411	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474384	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1475593	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1524929	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1735136	0.83[CHB][hapmap]
rs1735137	0.81[CHB][hapmap]
rs2009713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026268	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2037668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2178881	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2246616	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]
rs2837043	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837045	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837046	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2837047	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837048	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2837049	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2837050	1.00[ASN][1000 genomes]
rs2837051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837052	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837053	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2837054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837055	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28634277	0.98[ASN][1000 genomes]
rs3787927	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4118060	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816629	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818038	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818039	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818040	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818041	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4818042	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818045	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6517551	0.83[CHB][hapmap]
rs6517552	0.81[CHB][hapmap]
rs6517553	1.00[ASN][1000 genomes]
rs7277107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7278885	0.95[ASN][1000 genomes]
rs7280971	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7281076	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8126715	0.97[ASN][1000 genomes]
rs8126729	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8126860	1.00[ASN][1000 genomes]
rs8127748	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128567	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8128795	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8131355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132867	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133292	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8133862	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9976202	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9976208	0.82[CEU][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9982529	0.81[CHB][hapmap]
rs9983297	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9984540	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1067330	chr21:40841948-40879552	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2755103	chr21:40847196-40877805	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9983428	LCA5L	cis	Thyroid	GTEx
rs9983428	SH3BGR	cis	Thyroid	GTEx
rs9983428	LCA5L	cis	lung	GTEx
rs9983428	LCA5L	cis	Muscle Skeletal	GTEx
rs9983428	LCA5L	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
3	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr21:40872000-40875200	Enhancers	Psoas Muscle	Psoas
5	chr21:40872600-40878400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr21:40872800-40875800	Weak transcription	Left Ventricle	heart
7	chr21:40873000-40876200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr21:40874000-40875200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr21:40874000-40875800	Enhancers	Brain Substantia Nigra	brain
10	chr21:40874000-40877200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr21:40874200-40875600	Enhancers	Brain Anterior Caudate	brain
12	chr21:40874200-40875600	Enhancers	Brain Cingulate Gyrus	brain
13	chr21:40874200-40876200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr21:40874400-40875200	Enhancers	Brain Angular Gyrus	brain
15	chr21:40874400-40875400	Enhancers	Brain Hippocampus Middle	brain
16	chr21:40874400-40875600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr21:40874600-40875600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr21:40874600-40875600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr21:40874600-40875800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr21:40874600-40875800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr21:40874600-40876600	Enhancers	Fetal Heart	heart
22	chr21:40874600-40883000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:40874800-40887000	Weak transcription	Aorta	Aorta
24	chr21:40875000-40875400	Enhancers	Fetal Lung	lung
25	chr21:40875000-40875400	Weak transcription	Pancreas	Pancrea
26	chr21:40875000-40875600	Enhancers	Primary monocytes fromperipheralblood	blood

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