Variant report

Variant	rs3746992
Chromosome Location	chr21:47404043-47404044
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr21:47404038-47404214	Hela-S3	cervix:	n/a	n/a
2	UBTF	chr21:47404028-47404244	K562	blood:	n/a	n/a
3	YY1	chr21:47403911-47404286	K562	blood:	n/a	chr21:47404136-47404150
4	MAZ	chr21:47403983-47404244	K562	blood:	n/a	n/a
5	MAZ	chr21:47404035-47404131	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr21:47404020-47404170	AG09319	gingival:	n/a	chr21:47404136-47404149
7	CTCF	chr21:47404027-47404199	Fibrobl	skin:	n/a	chr21:47404136-47404149
8	E2F6	chr21:47404002-47404413	K562	blood:	n/a	n/a
9	FOXP2	chr21:47403911-47404224	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr21:47403910-47404591	IMR90	lung:	n/a	n/a
11	POLR2A	chr21:47403849-47404409	ProgFib	skin:	n/a	n/a
12	MAX	chr21:47403925-47404541	K562	blood:	n/a	chr21:47404392-47404402
13	YY1	chr21:47403989-47404221	K562	blood:	n/a	chr21:47404136-47404150
14	HMGN3	chr21:47404011-47404421	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:47334656..47336650-chr21:47402926..47405175,2	MCF-7	breast:
2	chr21:47402572..47405446-chr21:47518065..47519578,2	MCF-7	breast:
3	chr21:47402054..47404414-chr21:47532633..47534962,2	K562	blood:
4	chr12:50057880..50060234-chr21:47402833..47404920,2	MCF-7	breast:

Variant related genes	Relation type
COL6A1	TF binding region
ENSG00000142173	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1076608	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12482177	0.86[JPT][hapmap]
rs17551710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2839075	0.88[CEU][hapmap]
rs2839076	0.88[CEU][hapmap]
rs35383442	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35454297	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs754507	0.86[JPT][hapmap]
rs9754024	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9983378	1.00[CEU][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv914088	chr21:47358915-47419012	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
21	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
22	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
23	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
24	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
25	nsv587931	chr21:47393268-47412660	Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
26	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
27	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
28	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
29	nsv587932	chr21:47398411-47418311	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
30	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
31	nsv587933	chr21:47401193-47412703	Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
32	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3746992	COL6A1	cis	brain	BrainEAC

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47401000-47404200	Active TSS	Colon Smooth Muscle	Colon
2	chr21:47401200-47404400	Active TSS	HSMM	muscle
3	chr21:47401200-47407600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr21:47401400-47404200	Active TSS	Rectal Smooth Muscle	rectum
5	chr21:47401800-47404600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr21:47402200-47406200	Transcr. at gene 5' and 3'	NHLF	lung
7	chr21:47402400-47405400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr21:47402600-47405400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr21:47402600-47405600	Transcr. at gene 5' and 3'	Osteobl	bone
10	chr21:47402800-47404200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:47402800-47404200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr21:47402800-47404800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr21:47402800-47406000	Weak transcription	Liver	Liver
14	chr21:47402800-47406000	Weak transcription	Brain Hippocampus Middle	brain
15	chr21:47402800-47407600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr21:47403000-47404200	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr21:47403000-47404400	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:47403000-47404600	Weak transcription	Brain Angular Gyrus	brain
19	chr21:47403200-47404200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:47403200-47404400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr21:47403200-47404400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr21:47403200-47405000	Weak transcription	Brain Anterior Caudate	brain
23	chr21:47403200-47414600	Weak transcription	Brain Substantia Nigra	brain
24	chr21:47403200-47415200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr21:47403200-47424600	Weak transcription	Small Intestine	intestine
26	chr21:47403200-47425000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr21:47403400-47404200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr21:47403400-47404200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr21:47403400-47404200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr21:47403400-47404200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr21:47403400-47404200	Weak transcription	Brain Germinal Matrix	brain
32	chr21:47403400-47404200	Flanking Active TSS	Ovary	ovary
33	chr21:47403400-47404200	Active TSS	NHDF-Ad	bronchial
34	chr21:47403400-47404400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr21:47403400-47404600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr21:47403400-47404600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr21:47403400-47405400	Weak transcription	Fetal Brain Female	brain
38	chr21:47403400-47406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr21:47403400-47406000	Genic enhancers	Spleen	Spleen
40	chr21:47403600-47404200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr21:47403600-47404200	Weak transcription	Esophagus	oesophagus
42	chr21:47403600-47404200	Weak transcription	Lung	lung
43	chr21:47403600-47404200	Weak transcription	HSMMtube	muscle
44	chr21:47403600-47404400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr21:47403600-47404600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr21:47403600-47404600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr21:47403600-47404600	Weak transcription	Fetal Brain Male	brain
48	chr21:47403600-47404600	Strong transcription	Fetal Intestine Large	intestine
49	chr21:47403600-47404600	Weak transcription	Fetal Kidney	kidney
50	chr21:47403600-47404600	Genic enhancers	Fetal Muscle Trunk	muscle

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