Variant report

Variant	rs2178881
Chromosome Location	chr21:40844300-40844301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40843042..40844967-chr21:40948609..40950746,2	MCF-7	breast:
2	chr21:40842346..40845248-chr21:40847999..40850536,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11088478	0.95[ASN][1000 genomes]
rs11575944	0.80[AMR][1000 genomes]
rs11700626	1.00[LWK][hapmap]
rs11701190	0.94[ASN][1000 genomes]
rs11701232	0.94[ASN][1000 genomes]
rs11702769	0.96[ASN][1000 genomes]
rs12482418	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs13046275	0.99[ASN][1000 genomes]
rs13050145	0.95[ASN][1000 genomes]
rs13051411	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1474384	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1475593	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1524929	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2009713	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2026268	0.96[ASN][1000 genomes]
rs2037668	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2246616	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2837043	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2837045	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837046	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837047	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837048	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2837049	0.96[ASN][1000 genomes]
rs2837050	0.96[ASN][1000 genomes]
rs2837051	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2837052	0.96[ASN][1000 genomes]
rs2837053	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2837054	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2837055	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs28634277	0.98[ASN][1000 genomes]
rs3787927	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs4118060	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4816629	0.94[ASN][1000 genomes]
rs4818038	0.96[ASN][1000 genomes]
rs4818039	0.94[ASN][1000 genomes]
rs4818040	0.96[ASN][1000 genomes]
rs4818041	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4818042	0.96[ASN][1000 genomes]
rs4818044	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4818045	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4818046	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs502507	1.00[LWK][hapmap]
rs6517553	0.96[ASN][1000 genomes]
rs7277107	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7277633	0.81[ASN][1000 genomes]
rs7278885	0.94[ASN][1000 genomes]
rs7280971	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7281076	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8126715	0.93[ASN][1000 genomes]
rs8126729	0.96[ASN][1000 genomes]
rs8126860	0.96[ASN][1000 genomes]
rs8127748	0.96[ASN][1000 genomes]
rs8128567	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8128795	0.88[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8131355	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8132867	0.96[ASN][1000 genomes]
rs8132996	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8133292	0.95[ASN][1000 genomes]
rs8133862	0.96[ASN][1000 genomes]
rs9974333	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9976202	0.96[ASN][1000 genomes]
rs9976208	0.96[ASN][1000 genomes]
rs9983297	0.98[ASN][1000 genomes]
rs9983428	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9984540	1.00[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2178881	LCA5L	cis	Muscle Skeletal	GTEx
rs2178881	LCA5L	cis	Thyroid	GTEx
rs2178881	LCA5L	cis	parietal	SCAN
rs2178881	CBR1	cis	cerebellum	SCAN
rs2178881	WRB	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40824000-40852400	Weak transcription	Pancreas	Pancrea
2	chr21:40825000-40847800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr21:40826600-40849800	Weak transcription	HSMMtube	muscle
4	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr21:40828600-40847400	Weak transcription	Brain Substantia Nigra	brain
6	chr21:40828800-40847600	Weak transcription	Brain Angular Gyrus	brain
7	chr21:40828800-40847600	Weak transcription	Brain Anterior Caudate	brain
8	chr21:40829800-40856200	Weak transcription	Aorta	Aorta
9	chr21:40830200-40849800	Weak transcription	Primary T cells from cord blood	blood
10	chr21:40833000-40847200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr21:40835600-40851000	Weak transcription	Ovary	ovary
12	chr21:40835800-40847800	Weak transcription	Left Ventricle	heart
13	chr21:40836200-40851000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr21:40836200-40852200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr21:40836400-40851400	Weak transcription	Brain Hippocampus Middle	brain
16	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
17	chr21:40838800-40849800	Weak transcription	Liver	Liver
18	chr21:40840600-40847600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr21:40840600-40847800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr21:40844000-40844600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr21:40844000-40844800	Genic enhancers	Fetal Heart	heart
22	chr21:40844200-40844400	Genic enhancers	Psoas Muscle	Psoas
23	chr21:40844200-40844600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr21:40844200-40844600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:40844200-40844800	Enhancers	Skeletal Muscle Female	skeletal muscle

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