Variant report

Variant	rs3827246
Chromosome Location	chr21:45344799-45344800
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	KAP1	chr21:45344320-45344835	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45334297..45336681-chr21:45344684..45347847,3	MCF-7	breast:
2	chr21:45228584..45234568-chr21:45342221..45347972,7	K562	blood:
3	chr21:45284985..45287311-chr21:45344207..45345768,2	K562	blood:
4	chr21:45283663..45287678-chr21:45338795..45345768,12	K562	blood:

Variant related genes	Relation type
AGPAT3	TF binding region
ENSG00000160216	Chromatin interaction
ENSG00000215458	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1005192	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13052200	0.81[ASN][1000 genomes]
rs1573474	0.81[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs1888525	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070547	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838435	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838436	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838439	0.80[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819340	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4819345	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819348	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6518334	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs6518335	0.91[EUR][1000 genomes]
rs6518337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6518338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7275972	0.81[ASN][1000 genomes]
rs7276578	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762404	0.81[ASN][1000 genomes]
rs762411	0.86[JPT][hapmap]
rs762415	0.86[JPT][hapmap]
rs8127341	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8133789	0.81[ASN][1000 genomes]
rs914196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9306164	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9306165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9306166	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9974282	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9978688	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9985035	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs999519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3827246	TFF2	cis	cerebellum	SCAN
rs3827246	CSTB	cis	lymphoblastoid	seeQTL
rs3827246	ZNF295	cis	parietal	SCAN
rs3827246	ETS2	cis	parietal	SCAN
rs3827246	POFUT2	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45336400-45351600	Weak transcription	Fetal Brain Female	brain
2	chr21:45337200-45350800	Weak transcription	Fetal Brain Male	brain
3	chr21:45337600-45358600	Weak transcription	Osteobl	bone
4	chr21:45338800-45358600	Weak transcription	Hela-S3	cervix
5	chr21:45339800-45346400	Enhancers	Right Ventricle	heart
6	chr21:45340000-45344800	Enhancers	Fetal Muscle Trunk	muscle
7	chr21:45340000-45346400	Enhancers	Adipose Nuclei	Adipose
8	chr21:45340600-45346000	Enhancers	Esophagus	oesophagus
9	chr21:45340800-45358800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr21:45341000-45345200	Enhancers	Placenta	Placenta
11	chr21:45341000-45346200	Enhancers	Left Ventricle	heart
12	chr21:45341200-45344800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr21:45341400-45358600	Weak transcription	A549	lung
14	chr21:45341600-45344800	Enhancers	HepG2	liver
15	chr21:45341600-45345600	Enhancers	Fetal Heart	heart
16	chr21:45341600-45345800	Enhancers	Psoas Muscle	Psoas
17	chr21:45341800-45345200	Enhancers	Brain Anterior Caudate	brain
18	chr21:45342200-45357000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr21:45342200-45358800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr21:45342400-45345400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr21:45342400-45345800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:45342400-45348000	Weak transcription	Primary B cells from cord blood	blood
23	chr21:45342400-45348400	Weak transcription	Fetal Kidney	kidney
24	chr21:45342400-45356400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr21:45342600-45344800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr21:45342600-45345000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr21:45342600-45345400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr21:45342600-45347600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr21:45342600-45348000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr21:45342600-45350400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr21:45342600-45353000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr21:45342600-45354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:45342800-45345000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr21:45342800-45347600	Weak transcription	Aorta	Aorta
35	chr21:45342800-45350600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr21:45342800-45351000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr21:45343000-45345400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr21:45343000-45345600	Enhancers	Stomach Mucosa	stomach
39	chr21:45343000-45357600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr21:45343000-45372400	Weak transcription	Small Intestine	intestine
41	chr21:45343200-45345000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr21:45343200-45347400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr21:45343400-45345200	Genic enhancers	K562	blood
44	chr21:45343400-45355200	Weak transcription	Brain Germinal Matrix	brain
45	chr21:45343400-45355600	Weak transcription	Brain Angular Gyrus	brain
46	chr21:45343600-45345200	Enhancers	Brain Cingulate Gyrus	brain
47	chr21:45343600-45347400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr21:45343600-45347600	Weak transcription	NHLF	lung
49	chr21:45343600-45349800	Strong transcription	GM12878-XiMat	blood
50	chr21:45343600-45358000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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