Variant report

Variant	rs9983180
Chromosome Location	chr21:40817071-40817072
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr21:40817050-40818075	K562	blood:	n/a	n/a
2	MXI1	chr21:40817025-40818197	K562	blood:	n/a	n/a
3	NR2F2	chr21:40816977-40818203	MCF-7	breast:	n/a	n/a
4	SIN3AK20	chr21:40816970-40818280	MCF-7	breast:	n/a	n/a
5	POLR2A	chr21:40816598-40818147	IMR90	lung:	n/a	n/a
6	POLR2A	chr21:40816939-40817109	ProgFib	skin:	n/a	n/a
7	MYC	chr21:40816901-40818552	K562	blood:	n/a	chr21:40817927-40817936
8	HCFC1	chr21:40817066-40818622	Hela-S3	cervix:	n/a	n/a
9	GATA2	chr21:40816678-40817858	SH-SY5Y	brain:	n/a	chr21:40817179-40817187
10	MAZ	chr21:40816767-40818164	IMR90	lung:	n/a	chr21:40817927-40817936
11	ZNF143	chr21:40817043-40818372	K562	blood:	n/a	chr21:40817746-40817756
12	SMARCC1	chr21:40816551-40818214	Hela-S3	cervix:	n/a	n/a
13	MYC	chr21:40817045-40818471	K562	blood:	n/a	chr21:40817927-40817936
14	MAX	chr21:40816977-40818119	K562	blood:	n/a	chr21:40817927-40817936
15	GATA3	chr21:40816974-40817303	T-47D	breast:	n/a	chr21:40817179-40817187
16	MXI1	chr21:40816468-40818248	IMR90	lung:	n/a	n/a
17	REST	chr21:40816476-40818393	H1-neurons	neurons:	n/a	n/a
18	SIN3A	chr21:40817051-40818356	H1-hESC	embryonic stem cell:	n/a	chr21:40817349-40817362 chr21:40817749-40817762 chr21:40817749-40817760
19	POLR2A	chr21:40816944-40817136	MCF10A-Er-Src	breast:	n/a	n/a
20	MXI1	chr21:40816307-40818898	SK-N-SH	brain:	n/a	n/a
21	MAX	chr21:40817066-40818229	NB4	blood:	n/a	chr21:40817927-40817936
22	HCFC1	chr21:40816914-40818182	K562	blood:	n/a	n/a
23	TEAD4	chr21:40816477-40818634	K562	blood:	n/a	n/a
24	BRCA1	chr21:40816496-40817143	Hela-S3	cervix:	n/a	n/a
25	SIN3AK20	chr21:40816478-40818410	MCF-7	breast:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40552682..40557091-chr21:40814575..40819975,14	K562	blood:
2	chr21:40570372..40572709-chr21:40816957..40818525,2	MCF-7	breast:
3	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
4	chr21:40750443..40753981-chr21:40814998..40818130,3	MCF-7	breast:
5	chr21:40808402..40815127-chr21:40815513..40821149,12	K562	blood:
6	chr21:40552682..40557546-chr21:40815502..40820280,12	K562	blood:
7	chr21:40758092..40760884-chr21:40816362..40818206,3	K562	blood:
8	chr21:40684107..40685647-chr21:40816624..40819498,2	K562	blood:
9	chr21:40782804..40784995-chr21:40816330..40818172,2	K562	blood:
10	chr21:40553976..40556398-chr21:40816228..40819085,2	MCF-7	breast:
11	chr21:40758008..40760801-chr21:40816074..40819285,3	MCF-7	breast:
12	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
13	chr21:40719979..40722729-chr21:40816056..40819504,5	MCF-7	breast:
14	chr21:40759156..40760884-chr21:40816362..40818324,3	K562	blood:
15	chr21:40808687..40811589-chr21:40816980..40819320,3	K562	blood:
16	chr21:40720623..40723017-chr21:40815562..40818761,4	K562	blood:
17	chr21:40683731..40685549-chr21:40816150..40817682,2	MCF-7	breast:
18	chr21:40555615..40557158-chr21:40816762..40818748,2	MCF-7	breast:
19	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
20	chr21:40816254..40817919-chr21:40832845..40834906,2	MCF-7	breast:
21	chr21:40683837..40687545-chr21:40816624..40819639,6	K562	blood:

No data

Variant related genes	Relation type
LCA5L	TF binding region
SH3BGR	TF binding region
ENSG00000185658	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11575944	0.95[ASN][1000 genomes]
rs12483547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13050837	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051054	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051142	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2009713	0.82[TSI][hapmap]
rs2049823	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837010	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2837011	0.82[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2837012	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2837013	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2837014	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2837016	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs2837027	0.88[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2837028	0.83[ASN][1000 genomes]
rs2837033	0.86[ASN][1000 genomes]
rs2837038	0.88[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4816626	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4816628	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7276842	0.85[ASN][1000 genomes]
rs7277602	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7277633	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130381	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9979289	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9979353	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9983100	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9983435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs9983716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs9983180	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs9983180	WRB	cis	Artery Tibial	GTEx
rs9983180	WRB	cis	cerebellum	SCAN
rs9983180	WRB	cis	Thyroid	GTEx
rs9983180	WRB	cis	parietal	SCAN
rs9983180	LCA5L	cis	lung	GTEx
rs9983180	LCA5L	cis	Nerve Tibial	GTEx
rs9983180	LCA5L	cis	Stomach	GTEx
rs9983180	WRB	cis	multi-tissue	Pritchard
rs9983180	HMGN1	cis	lymphoblastoid	seeQTL
rs9983180	LCA5L	cis	Muscle Skeletal	GTEx
rs9983180	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs9983180	C21orf121	cis	cerebellum	SCAN
rs9983180	LCA5L	cis	Esophagus Mucosa	GTEx
rs9983180	WRB	cis	lung	GTEx
rs9983180	LCA5L	cis	Artery Tibial	GTEx
rs9983180	LCA5L	cis	Thyroid	GTEx
rs9983180	LCA5L	cis	Adipose Subcutaneous	GTEx
rs9983180	LCA5L	cis	Esophagus Muscularis	GTEx
rs9983180	LCA5L	cis	Artery Aorta	GTEx
rs9983180	LCA5L	cis	parietal	SCAN
rs9983180	SH3BGR	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40816400-40817200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr21:40816400-40817200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr21:40816400-40817200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr21:40816400-40817200	Enhancers	Spleen	Spleen
5	chr21:40816400-40818200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr21:40816400-40818200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr21:40816600-40817200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr21:40816600-40817200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:40816600-40817200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr21:40816600-40817200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr21:40816600-40817200	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr21:40816600-40817200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr21:40816600-40817200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr21:40816600-40817200	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr21:40816600-40817200	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr21:40816600-40817200	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr21:40816600-40817200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr21:40816600-40817200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr21:40816600-40817200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr21:40816600-40817200	Flanking Active TSS	Fetal Brain Male	brain
21	chr21:40816600-40817200	Enhancers	Gastric	stomach
22	chr21:40816600-40817200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr21:40816600-40817200	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr21:40816600-40817200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr21:40816600-40817200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr21:40816600-40817200	Enhancers	Small Intestine	intestine
27	chr21:40816600-40817200	Flanking Active TSS	GM12878-XiMat	blood
28	chr21:40816600-40817200	Flanking Active TSS	Hela-S3	cervix
29	chr21:40816600-40817200	Flanking Active TSS	HUVEC	blood vessel
30	chr21:40816600-40817200	Flanking Active TSS	K562	blood
31	chr21:40816600-40817200	Flanking Active TSS	NH-A	brain
32	chr21:40816600-40817200	Flanking Active TSS	NHEK	skin
33	chr21:40816600-40817400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr21:40816600-40817400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr21:40816600-40817400	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr21:40816600-40817400	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr21:40816600-40817400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr21:40816600-40817400	Flanking Active TSS	Dnd41	blood
39	chr21:40816600-40818200	Active TSS	H9 Cell Line	embryonic stem cell
40	chr21:40816600-40818200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr21:40816600-40818400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr21:40816600-40818400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr21:40816600-40818400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr21:40816600-40818600	Active TSS	Brain Cingulate Gyrus	brain
45	chr21:40816800-40817200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr21:40816800-40817200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr21:40816800-40817200	Flanking Active TSS	Liver	Liver
48	chr21:40816800-40817200	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr21:40816800-40817200	Flanking Active TSS	Fetal Thymus	thymus
50	chr21:40816800-40817400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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