Variant report

Variant	rs2838392
Chromosome Location	chr21:45231959-45231960
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:45231596-45232309	GM12892	blood:	n/a	n/a
2	POLR2A	chr21:45227444-45233850	K562	blood:	n/a	n/a
3	POLR2A	chr21:45227484-45232123	K562	blood:	n/a	n/a
4	POLR2A	chr21:45231786-45231972	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr21:45228765-45232382	GM12891	blood:	n/a	n/a
6	USF1	chr21:45231936-45232436	ECC-1	luminal epithelium:	n/a	chr21:45232209-45232220
7	POLR2A	chr21:45231579-45232477	HL-60	blood:	n/a	n/a
8	POLR2A	chr21:45227647-45232825	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr21:45231319-45232438	GM12891	blood:	n/a	n/a
10	POLR2A	chr21:45231654-45232531	GM12878	blood:	n/a	n/a
11	EBF1	chr21:45231921-45232249	GM12878	blood:	n/a	n/a
12	POLR2A	chr21:45231381-45232310	GM12878	blood:	n/a	n/a
13	POLR2A	chr21:45231429-45232185	HepG2	liver:	n/a	n/a
14	POLR2A	chr21:45228627-45232093	K562	blood:	n/a	n/a
15	POLR2A	chr21:45231750-45232066	GM12892	blood:	n/a	n/a
16	CTCF	chr21:45231820-45231970	K562	blood:	n/a	n/a
17	CEBPB	chr21:45231939-45232247	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45226367..45233141-chr21:45284145..45288607,11	K562	blood:
2	chr21:45230413..45233240-chr21:45552025..45554993,2	MCF-7	breast:
3	chr21:45202942..45205405-chr21:45231641..45234246,2	K562	blood:
4	chr21:45226284..45237567-chr21:45281864..45289573,19	K562	blood:
5	chr21:45230580..45232122-chr21:45429937..45432486,2	K562	blood:
6	chr21:45228592..45232844-chr21:45283509..45286625,5	MCF-7	breast:
7	chr21:45228584..45234568-chr21:45342221..45347972,7	K562	blood:
8	chr21:45230337..45232483-chr21:45365596..45368025,2	K562	blood:
9	chr21:45229749..45232080-chr21:45430603..45432486,2	K562	blood:
10	chr21:45156182..45158069-chr21:45230385..45232004,2	K562	blood:
11	chr21:45231740..45232316-chr21:45358668..45359330,2	MCF-7	breast:
12	chr21:45230529..45232410-chr21:45493973..45496831,2	MCF-7	breast:
13	chr21:45229004..45230702-chr21:45230841..45232657,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215458	TF binding region
ENSG00000215458	Chromatin interaction
ENSG00000160216	Chromatin interaction
ENSG00000234030	Chromatin interaction
ENSG00000160218	Chromatin interaction
ENSG00000160221	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17004508	0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28581805	1.00[ASN][1000 genomes]
rs58194014	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58549917	1.00[ASN][1000 genomes]
rs743467	1.00[ASN][1000 genomes]
rs8128568	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv913879	chr21:45145286-45237039	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv913880	chr21:45145286-45263920	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv913881	chr21:45145286-45267193	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
7	nsv470904	chr21:45151045-45258047	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
9	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
11	nsv520305	chr21:45175958-45246326	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv913883	chr21:45191139-45252838	Weak transcription Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv913884	chr21:45191139-45255836	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv544469	chr21:45194085-45257959	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv913885	chr21:45206355-45249474	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv587718	chr21:45210932-45252838	Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1065007	chr21:45212880-45257959	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv544470	chr21:45212880-45257959	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv459292	chr21:45218440-45269841	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv587719	chr21:45218440-45269841	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	nsv522204	chr21:45220483-45246326	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv913886	chr21:45220483-45267193	Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
24	esv1844567	chr21:45230974-45246326	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838392	SLC5A3	trans	brain	seeQTL
rs2838392	DDX6	trans	brain	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45211000-45257200	Weak transcription	Right Atrium	heart
2	chr21:45221800-45234200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr21:45224600-45232200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:45224600-45234600	Weak transcription	Hela-S3	cervix
5	chr21:45224800-45234200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:45224800-45238400	Weak transcription	Aorta	Aorta
7	chr21:45226200-45234200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr21:45226400-45234400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr21:45226600-45232200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr21:45226600-45234800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr21:45226800-45232000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr21:45226800-45234400	Weak transcription	Brain Germinal Matrix	brain
13	chr21:45226800-45234800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr21:45229200-45232600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr21:45229200-45232800	Enhancers	Ovary	ovary
16	chr21:45229400-45232000	Enhancers	Placenta	Placenta
17	chr21:45229600-45232200	Weak transcription	Thymus	Thymus
18	chr21:45229600-45232800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr21:45229800-45237000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr21:45230200-45232400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:45230200-45232800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr21:45230200-45232800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr21:45230200-45233000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr21:45230200-45233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr21:45230400-45232600	Enhancers	Fetal Thymus	thymus
26	chr21:45230400-45232600	Enhancers	Gastric	stomach
27	chr21:45230600-45232000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr21:45230600-45232000	Enhancers	NHDF-Ad	bronchial
29	chr21:45230600-45232200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr21:45230600-45232400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr21:45230600-45232400	Enhancers	A549	lung
32	chr21:45230600-45232600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr21:45230600-45232600	Flanking Active TSS	Colonic Mucosa	Colon
34	chr21:45230600-45232600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr21:45230600-45232800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr21:45230600-45232800	Enhancers	Brain Substantia Nigra	brain
37	chr21:45230600-45232800	Enhancers	Fetal Lung	lung
38	chr21:45230800-45232400	Bivalent Enhancer	Fetal Stomach	stomach
39	chr21:45230800-45233200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr21:45230800-45233200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr21:45230800-45233200	Enhancers	Lung	lung
42	chr21:45231000-45232200	Enhancers	Brain Hippocampus Middle	brain
43	chr21:45231000-45232400	Active TSS	Rectal Smooth Muscle	rectum
44	chr21:45231000-45232600	Flanking Active TSS	HMEC	breast
45	chr21:45231000-45234400	Weak transcription	Fetal Brain Male	brain
46	chr21:45231200-45232000	Weak transcription	Brain Anterior Caudate	brain
47	chr21:45231200-45232200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr21:45231200-45232200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr21:45231200-45232400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr21:45231200-45232400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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