Variant report

Variant	rs2838799
Chromosome Location	chr21:46596977-46596978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46586995..46592553-chr21:46595453..46599761,7	K562	blood:
2	chr21:46596731..46599349-chr21:46833672..46835345,2	K562	blood:
3	chr21:46596742..46598458-chr21:46604486..46606241,2	MCF-7	breast:
4	chr21:46592424..46595013-chr21:46596357..46598792,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11088983	0.95[CEU][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11700834	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13051236	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1537121	0.86[EUR][1000 genomes]
rs1537122	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537123	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071873	0.85[AFR][1000 genomes]
rs2225434	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246081	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838800	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838806	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838813	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838815	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838818	0.80[GIH][hapmap];0.83[MEX][hapmap]
rs2849618	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367986	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs372766	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs373037	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs374778	0.82[EUR][1000 genomes]
rs377524	0.84[CEU][hapmap]
rs377902	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788183	0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs381466	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs384876	0.82[EUR][1000 genomes]
rs386762	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs394608	0.83[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs394872	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs395761	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs397092	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs399185	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs407133	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs412646	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs414715	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs421716	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs422720	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs422870	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs427943	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs434492	0.82[EUR][1000 genomes]
rs446158	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs4818766	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4819034	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8134836	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs914206	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs983157	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs984791	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9980766	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	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
3	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	esv1802303	chr21:46580319-46606676	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838799	C21orf58	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr21:46572400-46601000	Weak transcription	Fetal Brain Female	brain
3	chr21:46572800-46604800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr21:46575000-46601000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr21:46575400-46604800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr21:46582600-46598000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr21:46583800-46606000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr21:46587200-46600200	Weak transcription	Liver	Liver
9	chr21:46588200-46604800	Weak transcription	NHLF	lung
10	chr21:46588600-46601000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr21:46588600-46601400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr21:46589000-46606400	Weak transcription	Brain Substantia Nigra	brain
13	chr21:46589000-46646000	Weak transcription	Colonic Mucosa	Colon
14	chr21:46589600-46604600	Weak transcription	Osteobl	bone
15	chr21:46589800-46600200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr21:46589800-46602400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr21:46589800-46604800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr21:46589800-46604800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr21:46590000-46604800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr21:46590000-46605000	Weak transcription	Psoas Muscle	Psoas
21	chr21:46590000-46608800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr21:46590800-46607000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr21:46591000-46605000	Strong transcription	HSMM	muscle
24	chr21:46591200-46601600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr21:46591400-46605000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr21:46591400-46605800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr21:46592200-46601000	Weak transcription	Thymus	Thymus
28	chr21:46593400-46600200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr21:46594400-46604800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr21:46594600-46598000	Strong transcription	Hela-S3	cervix
31	chr21:46594800-46601000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr21:46595200-46605000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr21:46595400-46602000	Strong transcription	Fetal Stomach	stomach
34	chr21:46595400-46603600	Strong transcription	HSMMtube	muscle
35	chr21:46595600-46597200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr21:46595600-46597200	Strong transcription	Brain Germinal Matrix	brain
37	chr21:46595600-46597200	Strong transcription	Pancreas	Pancrea
38	chr21:46595600-46597400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr21:46595600-46597400	Strong transcription	HMEC	breast
40	chr21:46595600-46598400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr21:46595600-46598400	Strong transcription	Gastric	stomach
42	chr21:46595600-46599200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr21:46595600-46599600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr21:46595600-46601600	Strong transcription	Lung	lung
45	chr21:46595600-46602000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr21:46595600-46602000	Strong transcription	Fetal Intestine Small	intestine
47	chr21:46595600-46602200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr21:46595600-46602200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr21:46595600-46602400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr21:46595600-46602600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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