Variant report

Variant	rs13051054
Chromosome Location	chr21:40817507-40817508
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:362)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:362 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr21:40817210-40818167	Hela-S3	cervix:	n/a	chr21:40817927-40817936
2	POLR2A	chr21:40817365-40818110	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr21:40817442-40818083	GM19193	blood:	n/a	n/a
4	EP300	chr21:40817388-40817934	HepG2	liver:	n/a	chr21:40817786-40817802 chr21:40817739-40817755
5	RCOR1	chr21:40817421-40818071	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr21:40817390-40818067	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAFK	chr21:40817466-40817639	K562	blood:	n/a	n/a
8	MYC	chr21:40817337-40818462	NB4	blood:	n/a	chr21:40817927-40817936
9	JUND	chr21:40817499-40817804	A549	lung:	n/a	n/a
10	POLR2A	chr21:40817220-40818107	NB4	blood:	n/a	n/a
11	CTCF	chr21:40817500-40817650	SAEC	small airway:	n/a	n/a
12	CTCF	chr21:40817420-40817570	HRE	kidney:	n/a	n/a
13	E2F4	chr21:40817353-40818037	MCF10A-Er-Src	breast:	n/a	chr21:40817761-40817770 chr21:40817746-40817756
14	SIN3AK20	chr21:40817416-40817719	PANC-1	pancreas:	n/a	n/a
15	CTCF	chr21:40817380-40817530	HEK293	kidney:	n/a	n/a
16	POLR2A	chr21:40817303-40818089	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr21:40817213-40818200	H1-neurons	neurons:	n/a	n/a
18	TBP	chr21:40817456-40818257	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr21:40817244-40818209	MCF-7	breast:	n/a	n/a
20	CCNT2	chr21:40817050-40818075	K562	blood:	n/a	n/a
21	POLR2A	chr21:40817422-40818424	MCF10A-Er-Src	breast:	n/a	n/a
22	MAX	chr21:40817430-40818159	SK-N-SH	brain:	n/a	chr21:40817927-40817936
23	EP300	chr21:40817396-40817886	ECC-1	luminal epithelium:	n/a	chr21:40817786-40817802 chr21:40817739-40817755
24	MAZ	chr21:40817103-40818110	K562	blood:	n/a	chr21:40817927-40817936
25	CTCF	chr21:40817460-40817610	BJ	skin:	n/a	n/a
26	CTCF	chr21:40817440-40817590	GM12864	blood:	n/a	n/a
27	CTCF	chr21:40817440-40817590	GM12873	blood:	n/a	n/a
28	GABPA	chr21:40817296-40818097	K562	blood:	n/a	chr21:40817760-40817774 chr21:40817760-40817769 chr21:40817762-40817771 chr21:40817757-40817771 chr21:40817760-40817771
29	MXI1	chr21:40817025-40818197	K562	blood:	n/a	n/a
30	CTCF	chr21:40817380-40817530	Caco-2	colon:	n/a	n/a
31	FOXA1	chr21:40817461-40817939	T-47D	breast:	n/a	n/a
32	POLR2A	chr21:40817458-40818105	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr21:40817420-40817570	HepG2	liver:	n/a	n/a
34	NR2F2	chr21:40816977-40818203	MCF-7	breast:	n/a	n/a
35	POLR2A	chr21:40817248-40818167	Hela-S3	cervix:	n/a	n/a
36	HDAC2	chr21:40817313-40818095	H1-hESC	embryonic stem cell:	n/a	chr21:40817760-40817769
37	CTCF	chr21:40817440-40817590	GM12874	blood:	n/a	n/a
38	SIN3AK20	chr21:40816970-40818280	MCF-7	breast:	n/a	n/a
39	POLR2A	chr21:40817410-40818209	K562	blood:	n/a	n/a
40	SMARCB1	chr21:40817251-40818077	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr21:40817396-40817583	NHEK	skin:	n/a	n/a
42	POLR2A	chr21:40817430-40818375	K562	blood:	n/a	n/a
43	CTCF	chr21:40817460-40817610	K562	blood:	n/a	n/a
44	CTCF	chr21:40817440-40817590	HCPEpiC	choroid plexus:	n/a	n/a
45	RCOR1	chr21:40817435-40818026	HepG2	liver:	n/a	n/a
46	POLR2A	chr21:40816598-40818147	IMR90	lung:	n/a	n/a
47	CTCF	chr21:40817400-40817550	AoAF	blood vessel:	n/a	n/a
48	POLR2A	chr21:40817371-40818169	GM12892	blood:	n/a	n/a
49	TAF1	chr21:40817301-40818159	H1-neurons	neurons:	n/a	n/a
50	CTCF	chr21:40817440-40817590	HPF	lung:	n/a	n/a

No data

(count:22 , 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	chr21:40684209..40686276-chr21:40817224..40819799,4	MCF-7	breast:
8	chr21:40758092..40760884-chr21:40816362..40818206,3	K562	blood:
9	chr21:40684107..40685647-chr21:40816624..40819498,2	K562	blood:
10	chr21:40782804..40784995-chr21:40816330..40818172,2	K562	blood:
11	chr21:40553976..40556398-chr21:40816228..40819085,2	MCF-7	breast:
12	chr21:40758008..40760801-chr21:40816074..40819285,3	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	chr21:40176263..40179138-chr21:40817088..40818717,2	K562	blood:
18	chr21:40683731..40685549-chr21:40816150..40817682,2	MCF-7	breast:
19	chr21:40555615..40557158-chr21:40816762..40818748,2	MCF-7	breast:
20	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
21	chr21:40816254..40817919-chr21:40832845..40834906,2	MCF-7	breast:
22	chr21:40683837..40687545-chr21:40816624..40819639,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGN1-3	chr21:40817376-40817659	NONHSAT082192

No data

Variant related genes	Relation type
SH3BGR	TF binding region
LCA5L	TF binding region
ENSG00000185437	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000255568	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11575944	0.95[ASN][1000 genomes]
rs12483547	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13050837	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051142	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049823	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837027	0.83[ASN][1000 genomes]
rs2837028	0.83[ASN][1000 genomes]
rs2837033	0.86[ASN][1000 genomes]
rs2837038	0.82[ASN][1000 genomes]
rs4816626	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4816628	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7276842	0.85[ASN][1000 genomes]
rs7277602	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7277633	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130381	0.85[AMR][1000 genomes]
rs9979289	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9979353	0.82[ASN][1000 genomes]
rs9983100	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983180	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983404	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9983716	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs13051054	LCA5L	cis	Artery Tibial	GTEx
rs13051054	LCA5L	cis	Muscle Skeletal	GTEx
rs13051054	SH3BGR	cis	Artery Tibial	GTEx
rs13051054	LCA5L	cis	Esophagus Muscularis	GTEx
rs13051054	LCA5L	cis	Thyroid	GTEx
rs13051054	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs13051054	LCA5L	cis	Adipose Subcutaneous	GTEx
rs13051054	WRB	cis	Thyroid	GTEx
rs13051054	LCA5L	cis	lung	GTEx
rs13051054	WRB	cis	lung	GTEx
rs13051054	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs13051054	LCA5L	cis	Artery Aorta	GTEx
rs13051054	LCA5L	cis	Stomach	GTEx
rs13051054	LCA5L	cis	Esophagus Mucosa	GTEx
rs13051054	SH3BGR	cis	Thyroid	GTEx
rs13051054	WRB	cis	Artery Tibial	GTEx
rs13051054	LCA5L	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40816400-40818200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr21:40816400-40818200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr21:40816600-40818200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr21:40816600-40818200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr21:40816600-40818400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr21:40816600-40818400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr21:40816600-40818400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr21:40816600-40818600	Active TSS	Brain Cingulate Gyrus	brain
9	chr21:40816800-40818000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr21:40816800-40818000	Active TSS	Fetal Heart	heart
11	chr21:40816800-40818000	Active TSS	HSMM	muscle
12	chr21:40816800-40818200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr21:40816800-40818200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr21:40816800-40818200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr21:40816800-40818200	Active TSS	Colonic Mucosa	Colon
16	chr21:40816800-40818200	Active TSS	Lung	lung
17	chr21:40816800-40818200	Active TSS	NHDF-Ad	bronchial
18	chr21:40816800-40818400	Active TSS	Brain Germinal Matrix	brain
19	chr21:40816800-40818400	Active TSS	Right Atrium	heart
20	chr21:40816800-40818400	Active TSS	A549	lung
21	chr21:40816800-40818400	Active TSS	HSMMtube	muscle
22	chr21:40816800-40818600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:40817000-40817600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr21:40817000-40817800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr21:40817000-40817800	Active TSS	Thymus	Thymus
26	chr21:40817000-40817800	Active TSS	HMEC	breast
27	chr21:40817000-40818000	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr21:40817000-40818000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr21:40817000-40818000	Active TSS	Muscle Satellite Cultured Cells	--
30	chr21:40817000-40818000	Active TSS	Fetal Lung	lung
31	chr21:40817000-40818000	Active TSS	Fetal Muscle Leg	muscle
32	chr21:40817000-40818000	Active TSS	Fetal Stomach	stomach
33	chr21:40817000-40818000	Active TSS	Osteobl	bone
34	chr21:40817000-40818200	Active TSS	H1 Cell Line	embryonic stem cell
35	chr21:40817000-40818200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr21:40817000-40818200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:40817000-40818200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr21:40817000-40818200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr21:40817000-40818200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr21:40817000-40818200	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr21:40817000-40818200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr21:40817000-40818200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr21:40817000-40818200	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr21:40817000-40818200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr21:40817000-40818200	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr21:40817000-40818200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr21:40817000-40818200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr21:40817000-40818200	Active TSS	Aorta	Aorta
49	chr21:40817000-40818200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:40817000-40818200	Active TSS	Esophagus	oesophagus

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