Variant report

Variant	rs13053065
Chromosome Location	chr21:47420723-47420724
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr21:47420573-47421022	ECC-1	luminal epithelium:	n/a	n/a
2	USF1	chr21:47420562-47421003	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr21:47420249-47420969	K562	blood:	n/a	n/a
4	E2F6	chr21:47420613-47420852	K562	blood:	n/a	n/a
5	USF1	chr21:47420608-47420990	ECC-1	luminal epithelium:	n/a	n/a
6	MYC	chr21:47420324-47420920	K562	blood:	n/a	n/a
7	MAX	chr21:47420635-47420873	K562	blood:	n/a	n/a
8	MAX	chr21:47420457-47421045	ECC-1	luminal epithelium:	n/a	n/a
9	USF1	chr21:47420653-47420853	K562	blood:	n/a	n/a
10	ZBTB7A	chr21:47420665-47421172	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCBP3-3	chr21:47420673-47420842	NONHSAT083008

No data

Variant related genes	Relation type
COL6A1	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1053312	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1053320	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11553518	0.83[ASN][1000 genomes]
rs13048481	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276255	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818812	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819179	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
2	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
4	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
6	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
8	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
9	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
10	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
11	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
12	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
13	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
14	nsv914085	chr21:47342116-47433055	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
15	esv1848879	chr21:47343462-47455584	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
16	nsv914086	chr21:47352625-47445184	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
17	nsv914087	chr21:47352625-47453954	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
18	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
19	nsv914089	chr21:47383056-47453954	ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
20	nsv914090	chr21:47383056-47465205	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
21	nsv914091	chr21:47383056-47483799	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
22	nsv587930	chr21:47389258-47423389	Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
23	esv1802000	chr21:47394780-47476081	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
24	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
25	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
26	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
27	esv1824109	chr21:47401282-47431018	Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
28	nsv587934	chr21:47406601-47423389	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
29	esv1849213	chr21:47406836-47455584	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
30	nsv459310	chr21:47409503-47488387	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
31	nsv587935	chr21:47409503-47488387	Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
32	nsv914092	chr21:47410931-47431031	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
33	nsv914093	chr21:47411988-47427839	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
34	nsv914094	chr21:47416324-47431031	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
35	nsv914095	chr21:47417611-47427839	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
36	nsv521579	chr21:47419012-47423389	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
37	nsv524388	chr21:47419012-47424346	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
38	nsv914096	chr21:47419066-47431031	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13053065	COL6A1	cis	temporal cortex	BrainEAC
rs13053065	COL6A1	cis	brain	BrainEAC

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47403200-47424600	Weak transcription	Small Intestine	intestine
2	chr21:47403200-47425000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr21:47404000-47424200	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr21:47404000-47424600	Strong transcription	Aorta	Aorta
5	chr21:47404200-47425200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr21:47404200-47425200	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr21:47405000-47423800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr21:47405000-47425400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr21:47405200-47425400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr21:47405200-47425400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:47405200-47425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr21:47405400-47423800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr21:47405400-47424800	Strong transcription	Fetal Brain Female	brain
14	chr21:47405400-47425200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr21:47405600-47423000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr21:47406400-47421400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr21:47406600-47425400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr21:47407600-47425000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr21:47408400-47425800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr21:47409000-47425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr21:47409200-47425000	Strong transcription	Ovary	ovary
22	chr21:47409800-47426600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr21:47410000-47422600	Weak transcription	Liver	Liver
24	chr21:47411200-47432800	Weak transcription	Right Atrium	heart
25	chr21:47412400-47423000	Strong transcription	Colonic Mucosa	Colon
26	chr21:47412400-47426400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr21:47412600-47422400	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:47412600-47425800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr21:47413800-47425200	Strong transcription	NHLF	lung
30	chr21:47414000-47421200	Strong transcription	Spleen	Spleen
31	chr21:47414200-47424800	Strong transcription	Right Ventricle	heart
32	chr21:47414600-47421200	Strong transcription	Placenta	Placenta
33	chr21:47414800-47425200	Strong transcription	Osteobl	bone
34	chr21:47415200-47425200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr21:47415400-47420800	Strong transcription	NHDF-Ad	bronchial
36	chr21:47415400-47422200	Weak transcription	HSMMtube	muscle
37	chr21:47415400-47423400	Weak transcription	HSMM	muscle
38	chr21:47415400-47424600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr21:47415400-47424600	Strong transcription	Adipose Nuclei	Adipose
40	chr21:47415400-47425000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr21:47415400-47425000	Weak transcription	Brain Anterior Caudate	brain
42	chr21:47415600-47425400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr21:47416000-47425400	Strong transcription	Fetal Intestine Small	intestine
44	chr21:47416200-47422800	Strong transcription	Colon Smooth Muscle	Colon
45	chr21:47416200-47425200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr21:47416400-47421200	Strong transcription	Lung	lung
47	chr21:47416400-47422000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr21:47416400-47425200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr21:47416400-47425400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr21:47416400-47425800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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