Variant report

Variant	rs12482177
Chromosome Location	chr21:47403435-47403436
allele	C/T
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	CTCF	chr21:47403360-47403510	AoAF	blood vessel:	n/a	chr21:47403437-47403450
2	CTCF	chr21:47403380-47403530	AG10803	skin:	n/a	chr21:47403437-47403450
3	CTCF	chr21:47403360-47403510	AG04450	lung:	n/a	chr21:47403437-47403450
4	CHD1	chr21:47401594-47403769	IMR90	lung:	n/a	n/a
5	MAZ	chr21:47400656-47403757	IMR90	lung:	n/a	chr21:47401469-47401478 chr21:47403308-47403318 chr21:47403612-47403621 chr21:47403387-47403397 chr21:47402689-47402698
6	CTCF	chr21:47403320-47403470	BJ	skin:	n/a	chr21:47403437-47403450
7	CTCF	chr21:47403340-47403490	HCFaa	heart:	n/a	chr21:47403437-47403450
8	CTCF	chr21:47403340-47403490	HPAF	blood vessel:	n/a	chr21:47403437-47403450
9	CTCF	chr21:47403360-47403510	AG04449	skin:	n/a	chr21:47403437-47403450
10	CTCF	chr21:47403340-47403490	HBMEC	blood vessel:	n/a	chr21:47403437-47403450
11	CTCF	chr21:47403400-47403550	HRE	kidney:	n/a	chr21:47403437-47403450
12	RAD21	chr21:47401019-47403535	IMR90	lung:	n/a	chr21:47402453-47402467 chr21:47403436-47403450
13	CTCF	chr21:47403424-47403527	IMR90	lung:	n/a	chr21:47403437-47403450
14	POLR2A	chr21:47400248-47403609	IMR90	lung:	n/a	n/a
15	POLR2A	chr21:47403393-47403718	ProgFib	skin:	n/a	n/a
16	MXI1	chr21:47401595-47403734	IMR90	lung:	n/a	n/a
17	CTCF	chr21:47403320-47403470	AG09319	gingival:	n/a	chr21:47403437-47403450
18	CTCF	chr21:47403300-47403450	HFF	foreskin:	n/a	chr21:47403437-47403450

No.	Distal block	Cell Line	Cell type
1	chr21:47401629..47403752-chr21:47406521..47408992,2	K562	blood:
2	chr21:47334656..47336650-chr21:47402926..47405175,2	MCF-7	breast:
3	chr21:47402572..47405446-chr21:47518065..47519578,2	MCF-7	breast:
4	chr21:47402054..47404414-chr21:47532633..47534962,2	K562	blood:
5	chr12:50057880..50060234-chr21:47402833..47404920,2	MCF-7	breast:
6	chr21:47401680..47403965-chr21:47408741..47410479,2	K562	blood:

Variant related genes	Relation type
COL6A1	TF binding region
ENSG00000142173	Chromatin interaction
ENSG00000142156	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17551710	0.86[JPT][hapmap]
rs1883048	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2481872	0.83[EUR][1000 genomes]
rs2839075	0.81[CHB][hapmap]
rs3746992	0.86[JPT][hapmap]
rs754507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671	0.92[ASN][1000 genomes]
rs9978314	0.82[CHD][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12482177	PCBP3	cis	cerebellum	SCAN
rs12482177	COL6A1	cis	cerebellum	SCAN
rs12482177	PLAC4	cis	cerebellum	SCAN
rs12482177	C21orf2	cis	cerebellum	SCAN
rs12482177	FAM3B	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47400800-47403600	Active TSS	Placenta Amnion	Placenta Amnion
2	chr21:47400800-47403800	Active TSS	Left Ventricle	heart
3	chr21:47401000-47403600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr21:47401000-47403600	Active TSS	Psoas Muscle	Psoas
5	chr21:47401000-47404000	Active TSS	Right Atrium	heart
6	chr21:47401000-47404200	Active TSS	Colon Smooth Muscle	Colon
7	chr21:47401200-47403600	Active TSS	Aorta	Aorta
8	chr21:47401200-47403600	Active TSS	Fetal Kidney	kidney
9	chr21:47401200-47404000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr21:47401200-47404000	Active TSS	Gastric	stomach
11	chr21:47401200-47404400	Active TSS	HSMM	muscle
12	chr21:47401200-47407600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr21:47401400-47403600	Active TSS	HSMMtube	muscle
14	chr21:47401400-47403800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr21:47401400-47404200	Active TSS	Rectal Smooth Muscle	rectum
16	chr21:47401800-47403600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
17	chr21:47401800-47404600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr21:47402000-47403600	Active TSS	Lung	lung
19	chr21:47402200-47403600	Flanking Bivalent TSS/Enh	Placenta	Placenta
20	chr21:47402200-47406200	Transcr. at gene 5' and 3'	NHLF	lung
21	chr21:47402400-47403800	Enhancers	Fetal Heart	heart
22	chr21:47402400-47405400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr21:47402600-47403600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:47402600-47403600	Active TSS	Esophagus	oesophagus
25	chr21:47402600-47403600	Enhancers	Fetal Brain Male	brain
26	chr21:47402600-47403800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
27	chr21:47402600-47404000	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr21:47402600-47405400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr21:47402600-47405600	Transcr. at gene 5' and 3'	Osteobl	bone
30	chr21:47402800-47403600	Active TSS	Fetal Lung	lung
31	chr21:47402800-47404200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr21:47402800-47404200	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr21:47402800-47404800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr21:47402800-47406000	Weak transcription	Liver	Liver
35	chr21:47402800-47406000	Weak transcription	Brain Hippocampus Middle	brain
36	chr21:47402800-47407600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:47403000-47403600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr21:47403000-47403600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr21:47403000-47403600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
40	chr21:47403000-47403800	Bivalent/Poised TSS	Colonic Mucosa	Colon
41	chr21:47403000-47404000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr21:47403000-47404000	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr21:47403000-47404200	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr21:47403000-47404400	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr21:47403000-47404600	Weak transcription	Brain Angular Gyrus	brain
46	chr21:47403200-47403600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr21:47403200-47403600	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr21:47403200-47403600	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr21:47403200-47403600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr21:47403200-47403600	Active TSS	Fetal Thymus	thymus

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