Variant report

Variant	rs2839159
Chromosome Location	chr21:47651943-47651944
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:47650121-47657023	K562	blood:	n/a	n/a
2	POLR2A	chr21:47650719-47652506	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:47651813-47652856	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr21:47651760-47652374	GM12892	blood:	n/a	n/a
5	POLR2A	chr21:47651879-47652367	K562	blood:	n/a	n/a
6	POLR2A	chr21:47651806-47652340	HL-60	blood:	n/a	n/a
7	POLR2A	chr21:47651812-47652328	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr21:47651711-47652262	GM12878	blood:	n/a	n/a
9	POLR2A	chr21:47651781-47652419	GM12892	blood:	n/a	n/a
10	POLR2A	chr21:47651769-47652029	GM12891	blood:	n/a	n/a
11	POLR2A	chr21:47651856-47652400	Hela-S3	cervix:	n/a	n/a
12	HCFC1	chr21:47651914-47651968	K562	blood:	n/a	n/a
13	POLR2A	chr21:47651857-47652439	K562	blood:	n/a	n/a
14	POLR2A	chr21:47651237-47653301	GM12891	blood:	n/a	n/a
15	POLR2A	chr21:47651878-47652411	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr21:47651184-47652887	GM12878	blood:	n/a	n/a
17	POLR2A	chr21:47651898-47652002	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr21:47651836-47653191	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr21:47651621-47652558	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr21:47651067-47652979	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47637510..47639750-chr21:47649696..47652340,2	K562	blood:
2	chr21:47649909..47652487-chr21:47692841..47694788,2	K562	blood:
3	chr21:47650505..47653057-chr21:47704999..47707978,4	K562	blood:
4	chr21:47646929..47655402-chr21:47657205..47667464,13	MCF-7	breast:
5	chr21:47649475..47654213-chr21:47668159..47671239,4	MCF-7	breast:
6	chr21:47646765..47648918-chr21:47650185..47652427,3	MCF-7	breast:
7	chr21:47647765..47652638-chr21:47704055..47705991,5	MCF-7	breast:

No data

Variant related genes	Relation type
LSS	TF binding region
ENSG00000228137	Chromatin interaction
ENSG00000182362	Chromatin interaction
ENSG00000160294	Chromatin interaction
ENSG00000160285	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11700727	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11700943	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11701000	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11702775	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11702846	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17176835	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17182788	0.81[AFR][1000 genomes]
rs17183130	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17183318	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2187119	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2298695	0.81[GIH][hapmap]
rs2839142	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2839179	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs2839193	1.00[YRI][hapmap]
rs56173768	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73144751	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73144753	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73144754	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73144764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
14	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
15	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
16	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
17	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
18	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
19	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
20	nsv914134	chr21:47632995-47712185	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	n/a
21	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2839159	PCNT	cis	parietal	SCAN
rs2839159	S100B	cis	parietal	SCAN
rs2839159	S100B	cis	cerebellum	SCAN
rs2839159	C21orf57	cis	parietal	SCAN
rs2839159	C21orf56	Cis_1M	lymphoblastoid	RTeQTL
rs2839159	C21orf57	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47649800-47652000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
2	chr21:47649800-47652400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
3	chr21:47649800-47652800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr21:47649800-47653200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chr21:47649800-47654000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr21:47649800-47654200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr21:47649800-47654400	Weak transcription	Aorta	Aorta
8	chr21:47649800-47654400	Weak transcription	Colonic Mucosa	Colon
9	chr21:47649800-47654400	Weak transcription	Right Ventricle	heart
10	chr21:47649800-47701600	Weak transcription	Right Atrium	heart
11	chr21:47650000-47652000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
12	chr21:47650000-47652000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr21:47650000-47652000	Weak transcription	Esophagus	oesophagus
14	chr21:47650000-47652000	Weak transcription	Lung	lung
15	chr21:47650000-47652000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr21:47650000-47652400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
17	chr21:47650000-47652400	Weak transcription	Placenta	Placenta
18	chr21:47650000-47652600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
19	chr21:47650000-47652600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr21:47650000-47652600	Weak transcription	HSMMtube	muscle
21	chr21:47650000-47652800	Weak transcription	Adipose Nuclei	Adipose
22	chr21:47650000-47653000	Weak transcription	Fetal Intestine Small	intestine
23	chr21:47650000-47653000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr21:47650000-47653200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:47650000-47653200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr21:47650000-47653200	Weak transcription	Pancreas	Pancrea
27	chr21:47650000-47653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr21:47650000-47653800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr21:47650000-47654000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr21:47650000-47654000	Weak transcription	Brain Angular Gyrus	brain
31	chr21:47650000-47654000	Weak transcription	Brain Substantia Nigra	brain
32	chr21:47650000-47654000	Weak transcription	Colon Smooth Muscle	Colon
33	chr21:47650000-47654200	Weak transcription	Gastric	stomach
34	chr21:47650000-47654200	Weak transcription	Psoas Muscle	Psoas
35	chr21:47650000-47654200	Weak transcription	Spleen	Spleen
36	chr21:47650000-47654400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr21:47650000-47658600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr21:47650000-47658600	Weak transcription	Small Intestine	intestine
39	chr21:47650000-47705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr21:47650200-47652000	Weak transcription	Thymus	Thymus
41	chr21:47650200-47652200	Weak transcription	Fetal Thymus	thymus
42	chr21:47650200-47652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr21:47650200-47652800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr21:47650200-47653400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr21:47650200-47653600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr21:47650200-47653600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr21:47650200-47653600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr21:47650200-47653600	Weak transcription	Fetal Kidney	kidney
49	chr21:47650200-47653800	Weak transcription	Brain Anterior Caudate	brain
50	chr21:47650200-47653800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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