Variant report

Variant	rs2838519
Chromosome Location	chr21:45615023-45615024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45566742..45569322-chr21:45613127..45615094,2	MCF-7	breast:
2	chr21:45586838..45589344-chr21:45614842..45616536,2	MCF-7	breast:
3	chr21:45610715..45617377-chr21:45717031..45721978,7	MCF-7	breast:
4	chr21:45612553..45615742-chr21:45666296..45670643,3	MCF-7	breast:
5	chr21:45614676..45619255-chr21:45657692..45665676,14	MCF-7	breast:
6	chr21:45612993..45620081-chr21:45620303..45625017,17	MCF-7	breast:
7	chr21:45567927..45569479-chr21:45614833..45617390,2	K562	blood:
8	chr21:45611519..45615384-chr21:45659181..45663993,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232124	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000160223	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2070551	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2070552	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2838516	0.82[CHB][hapmap];0.93[EUR][1000 genomes]
rs2838517	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs2838520	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2838521	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2876932	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35405602	0.82[EUR][1000 genomes]
rs3804031	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs3804032	0.84[EUR][1000 genomes]
rs4317019	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4380337	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4456788	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4635612	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7276302	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes]
rs7282490	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs743478	0.92[EUR][1000 genomes]
rs743479	0.96[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs762421	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs762422	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs762423	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8126495	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8127691	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8134436	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
12	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
13	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	esv3411301	chr21:45609579-45620771	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	esv3455479	chr21:45609616-45620726	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv3455480	chr21:45609633-45620722	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Ulcerative colitis	21297633	GWAS catalog
Crohn's disease	21102463	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2838519	WRB	cis	cerebellum	SCAN
rs2838519	KRTAP10-3	cis	cerebellum	SCAN
rs2838519	C21orf2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45610400-45615400	Enhancers	NHDF-Ad	bronchial
2	chr21:45610400-45616000	Weak transcription	Thymus	Thymus
3	chr21:45610800-45616600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr21:45610800-45617600	Enhancers	Placenta	Placenta
5	chr21:45611200-45616200	Weak transcription	Gastric	stomach
6	chr21:45611600-45615200	Enhancers	Colon Smooth Muscle	Colon
7	chr21:45611600-45615400	Enhancers	Brain Anterior Caudate	brain
8	chr21:45612000-45616200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:45612200-45615800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:45612200-45617200	Enhancers	Fetal Muscle Leg	muscle
11	chr21:45612400-45615600	Enhancers	Fetal Stomach	stomach
12	chr21:45612400-45616400	Weak transcription	Esophagus	oesophagus
13	chr21:45612600-45615400	Enhancers	Fetal Lung	lung
14	chr21:45612600-45616000	Enhancers	Fetal Muscle Trunk	muscle
15	chr21:45612600-45616400	Weak transcription	Right Ventricle	heart
16	chr21:45612800-45615400	Enhancers	Adipose Nuclei	Adipose
17	chr21:45612800-45616000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr21:45612800-45616000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr21:45612800-45616000	Weak transcription	Left Ventricle	heart
20	chr21:45612800-45617400	Enhancers	Primary hematopoietic stem cells	blood
21	chr21:45613200-45615600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr21:45613200-45617000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr21:45613600-45617200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:45613600-45617400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr21:45613600-45617400	Enhancers	Primary B cells from peripheral blood	blood
26	chr21:45613800-45615400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:45614000-45616000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr21:45614000-45617000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr21:45614000-45617200	Enhancers	GM12878-XiMat	blood
30	chr21:45614000-45617600	Enhancers	Primary B cells from cord blood	blood
31	chr21:45614200-45615200	Weak transcription	Fetal Intestine Large	intestine
32	chr21:45614200-45615600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr21:45614200-45616000	Weak transcription	Fetal Intestine Small	intestine
34	chr21:45614200-45616200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr21:45614400-45617400	Weak transcription	Brain Angular Gyrus	brain
36	chr21:45614600-45615200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr21:45614600-45615800	Weak transcription	K562	blood
38	chr21:45614600-45616000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr21:45614600-45616000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr21:45614600-45616000	Weak transcription	Stomach Mucosa	stomach
41	chr21:45614600-45616400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr21:45614600-45616600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr21:45614800-45615600	Weak transcription	Fetal Thymus	thymus
44	chr21:45614800-45615800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr21:45614800-45615800	Weak transcription	Spleen	Spleen
46	chr21:45614800-45616000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr21:45614800-45616400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr21:45614800-45616400	Weak transcription	Right Atrium	heart
49	chr21:45614800-45622400	Weak transcription	Pancreas	Pancrea
50	chr21:45615000-45615800	Weak transcription	Brain Substantia Nigra	brain

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