Variant report

Variant	rs10775662
Chromosome Location	chr21:40756675-40756676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40756239-40759236	HepG2	liver:	n/a	n/a
2	POLR2A	chr21:40756621-40758606	HepG2	liver:	n/a	n/a
3	HEY1	chr21:40756667-40758658	HepG2	liver:	n/a	n/a
4	POLR2A	chr21:40756585-40758739	HepG2	liver:	n/a	n/a
5	NR2F2	chr21:40756575-40757022	K562	blood:	n/a	n/a
6	FOS	chr21:40756555-40756948	HUVEC	blood vessel:	n/a	chr21:40756707-40756718 chr21:40756707-40756718 chr21:40756709-40756717
7	POLR2A	chr21:40756560-40757044	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr21:40756525-40758658	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
2	chr21:40750751..40754678-chr21:40755594..40761324,12	K562	blood:
3	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
4	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
5	chr21:40683979..40686074-chr21:40756001..40757599,2	K562	blood:
6	chr21:40755802..40758273-chr21:40758369..40760779,2	MCF-7	breast:
7	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
8	chr21:40693407..40696384-chr21:40756189..40758708,3	MCF-7	breast:
9	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
10	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
11	chr21:40750891..40755008-chr21:40755976..40761346,13	MCF-7	breast:
12	chr21:40754696..40757531-chr21:40758610..40760673,2	K562	blood:

No data

Variant related genes	Relation type
WRB	TF binding region
ENSG00000238556	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000238141	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1060180	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701047	0.85[EUR][1000 genomes]
rs13051571	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13051949	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13230	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094874	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2244352	0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs2299739	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2299741	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836994	0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2836995	0.92[CHB][hapmap]
rs2836996	0.93[CHB][hapmap]
rs2836997	0.88[CEU][hapmap];0.92[CHB][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836998	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836999	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837000	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837001	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837002	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837003	0.85[CHB][hapmap]
rs2837004	0.85[CHB][hapmap]
rs2837005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837006	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2837007	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2837008	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3787923	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3787924	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4816624	0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4818031	0.82[ASN][1000 genomes]
rs4818032	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4818033	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4818035	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4818036	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8131718	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9305674	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9974828	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	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
3	nsv1056452	chr21:40741893-40782587	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs10775662	LCA5L	cis	lung	GTEx
rs10775662	LCA5L	cis	Artery Aorta	GTEx
rs10775662	LCA5L	cis	Nerve Tibial	GTEx
rs10775662	WRB	cis	lung	GTEx
rs10775662	WRB	cis	Nerve Tibial	GTEx
rs10775662	LCA5L	cis	Esophagus Mucosa	GTEx
rs10775662	WRB	cis	Esophagus Mucosa	GTEx
rs10775662	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs10775662	LCA5L	cis	Esophagus Muscularis	GTEx
rs10775662	LCA5L	cis	Heart Left Ventricle	GTEx
rs10775662	LCA5L	cis	Whole Blood	GTEx
rs10775662	WRB	cis	Artery Aorta	GTEx
rs10775662	LCA5L	cis	Artery Tibial	GTEx
rs10775662	LCA5L	cis	Thyroid	GTEx
rs10775662	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs10775662	LCA5L	cis	Stomach	GTEx
rs10775662	WRB	cis	Thyroid	GTEx
rs10775662	WRB	cis	Artery Tibial	GTEx
rs10775662	WRB	cis	Whole Blood	GTEx
rs10775662	WRB	cis	Esophagus Muscularis	GTEx
rs10775662	WRB	cis	Adipose Subcutaneous	GTEx
rs10775662	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40753000-40758000	Weak transcription	Small Intestine	intestine
2	chr21:40753200-40756800	Weak transcription	Lung	lung
3	chr21:40753200-40757000	Weak transcription	Stomach Mucosa	stomach
4	chr21:40753200-40757200	Weak transcription	Gastric	stomach
5	chr21:40753200-40757400	Weak transcription	Left Ventricle	heart
6	chr21:40753200-40759400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:40753200-40759800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr21:40753400-40756800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:40753400-40756800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr21:40753400-40756800	Weak transcription	Fetal Intestine Large	intestine
11	chr21:40753400-40756800	Weak transcription	Pancreas	Pancrea
12	chr21:40753400-40756800	Weak transcription	GM12878-XiMat	blood
13	chr21:40753400-40756800	Weak transcription	HSMM	muscle
14	chr21:40753400-40757000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:40753400-40757000	Weak transcription	Colonic Mucosa	Colon
16	chr21:40753400-40757000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr21:40753400-40757000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr21:40753400-40757000	Weak transcription	Right Ventricle	heart
19	chr21:40753400-40757200	Weak transcription	Brain Angular Gyrus	brain
20	chr21:40753400-40757200	Weak transcription	Placenta	Placenta
21	chr21:40753400-40757200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr21:40753400-40757200	Weak transcription	Spleen	Spleen
23	chr21:40753400-40757400	Weak transcription	Fetal Kidney	kidney
24	chr21:40753400-40757400	Weak transcription	Psoas Muscle	Psoas
25	chr21:40753400-40757600	Weak transcription	Primary T cells from cord blood	blood
26	chr21:40753400-40757600	Weak transcription	Esophagus	oesophagus
27	chr21:40753400-40757600	Weak transcription	Fetal Lung	lung
28	chr21:40753400-40757600	Weak transcription	Fetal Thymus	thymus
29	chr21:40753400-40757600	Weak transcription	Right Atrium	heart
30	chr21:40753400-40757600	Weak transcription	Thymus	Thymus
31	chr21:40753400-40759400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr21:40753400-40759400	Weak transcription	Aorta	Aorta
33	chr21:40753400-40760200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr21:40753600-40756800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr21:40753600-40756800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr21:40753600-40756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr21:40753600-40756800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr21:40753600-40756800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr21:40753600-40756800	Weak transcription	NH-A	brain
40	chr21:40753600-40756800	Weak transcription	NHDF-Ad	bronchial
41	chr21:40753600-40756800	Weak transcription	NHLF	lung
42	chr21:40753600-40757000	Weak transcription	Fetal Stomach	stomach
43	chr21:40753600-40757000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr21:40753600-40757200	Weak transcription	Adipose Nuclei	Adipose
45	chr21:40753600-40757200	Weak transcription	Brain Anterior Caudate	brain
46	chr21:40753600-40757200	Weak transcription	Brain Hippocampus Middle	brain
47	chr21:40753600-40757200	Weak transcription	Brain Substantia Nigra	brain
48	chr21:40753600-40757200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr21:40753600-40757200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr21:40753600-40757200	Weak transcription	A549	lung

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