Variant report

Variant	rs2836998
Chromosome Location	chr21:40759882-40759883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:108)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:108 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr21:40759736-40759926	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr21:40759838-40760901	HEK293-T-REx	kidney:	n/a	n/a
3	POLR2A	chr21:40759424-40759889	A549	lung:	n/a	n/a
4	POLR2A	chr21:40759490-40760859	GM12892	blood:	n/a	n/a
5	RCOR1	chr21:40759400-40760859	K562	blood:	n/a	n/a
6	HEY1	chr21:40759271-40759987	HepG2	liver:	n/a	n/a
7	POLR2A	chr21:40759403-40759920	HL-60	blood:	n/a	n/a
8	POLR2A	chr21:40759317-40760271	Hela-S3	cervix:	n/a	n/a
9	HCFC1	chr21:40759378-40760920	K562	blood:	n/a	n/a
10	POLR2A	chr21:40759494-40759927	MCF-7	breast:	n/a	n/a
11	TAF1	chr21:40759607-40759941	A549	lung:	n/a	n/a
12	MAX	chr21:40759361-40761054	MCF-7	breast:	n/a	chr21:40759619-40759629 chr21:40759797-40759807
13	POLR2A	chr21:40759397-40760953	K562	blood:	n/a	n/a
14	MYC	chr21:40759142-40760885	K562	blood:	n/a	chr21:40759619-40759629 chr21:40759797-40759807
15	POLR2A	chr21:40759361-40759984	HepG2	liver:	n/a	n/a
16	TAF1	chr21:40759605-40760182	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr21:40759369-40760016	PFSK-1	brain:	n/a	n/a
18	MAZ	chr21:40759081-40760889	K562	blood:	n/a	chr21:40759619-40759629 chr21:40759797-40759807
19	SIN3AK20	chr21:40758852-40761087	MCF-7	breast:	n/a	n/a
20	MAZ	chr21:40759299-40760105	IMR90	lung:	n/a	chr21:40759619-40759629 chr21:40759797-40759807
21	POLR2A	chr21:40759315-40760866	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr21:40759609-40759893	GM12891	blood:	n/a	n/a
23	POLR2A	chr21:40759144-40759973	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr21:40759373-40759919	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr21:40759364-40759884	K562	blood:	n/a	n/a
26	EP300	chr21:40759286-40760803	K562	blood:	n/a	n/a
27	ELF1	chr21:40759417-40760938	GM12878	blood:	n/a	chr21:40760733-40760745
28	TAF1	chr21:40759576-40759914	GM12878	blood:	n/a	n/a
29	POLR2A	chr21:40759291-40760092	U87	brain:	n/a	n/a
30	TBP	chr21:40759570-40759955	Hela-S3	cervix:	n/a	n/a
31	IRF1	chr21:40759358-40759999	K562	blood:	n/a	n/a
32	POLR2A	chr21:40759270-40759953	HepG2	liver:	n/a	n/a
33	UBTF	chr21:40759683-40760916	K562	blood:	n/a	n/a
34	ZKSCAN1	chr21:40759426-40760886	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr21:40759357-40759936	ECC-1	luminal epithelium:	n/a	n/a
36	ZMIZ1	chr21:40759623-40760127	K562	blood:	n/a	n/a
37	UBTF	chr21:40759810-40760134	K562	blood:	n/a	n/a
38	TAF1	chr21:40759389-40759968	ECC-1	luminal epithelium:	n/a	n/a
39	MYC	chr21:40759452-40760914	NB4	blood:	n/a	chr21:40759619-40759629 chr21:40759797-40759807
40	POLR2A	chr21:40759376-40759934	GM18526	blood:	n/a	n/a
41	NRF1	chr21:40759299-40759983	SK-N-SH	brain:	n/a	chr21:40759686-40759697 chr21:40759688-40759697 chr21:40759686-40759700 chr21:40759686-40759697 chr21:40759686-40759695 chr21:40759683-40759697
42	POLR2A	chr21:40759355-40759941	GM19099	blood:	n/a	n/a
43	TBP	chr21:40759154-40759944	K562	blood:	n/a	n/a
44	POLR2A	chr21:40759259-40759969	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr21:40759376-40759929	GM15510	blood:	n/a	n/a
46	POLR2A	chr21:40759388-40760572	HepG2	liver:	n/a	n/a
47	IRF1	chr21:40758962-40760766	K562	blood:	n/a	chr21:40759162-40759174
48	TAF1	chr21:40759496-40759938	K562	blood:	n/a	n/a
49	POLR2A	chr21:40759335-40760824	Raji	blood:	n/a	n/a
50	MAX	chr21:40759385-40759892	K562	blood:	n/a	chr21:40759619-40759629 chr21:40759797-40759807

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
2	chr21:40759594..40762847-chr21:40823318..40826677,3	K562	blood:
3	chr21:40745293..40746195-chr21:40759850..40760932,7	MCF-7	breast:
4	chr21:40757591..40761225-chr21:40763023..40767191,7	K562	blood:
5	chr21:40693463..40696053-chr21:40759629..40761307,2	MCF-7	breast:
6	chr21:40758499..40762376-chr21:40796781..40799288,3	K562	blood:
7	chr21:40759156..40760884-chr21:40816362..40818324,3	K562	blood:
8	chr21:40746451..40749340-chr21:40759411..40761167,2	MCF-7	breast:
9	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
10	chr21:40750855..40754449-chr21:40757264..40761324,13	K562	blood:
11	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
12	chr21:40759725..40763162-chr21:40764409..40767950,4	K562	blood:
13	chr21:40552516..40555515-chr21:40758943..40760790,2	MCF-7	breast:
14	chr21:40750751..40754678-chr21:40755594..40761324,12	K562	blood:
15	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
16	chr21:40552621..40555799-chr21:40758034..40760615,3	K562	blood:
17	chr21:40748679..40750814-chr21:40758912..40761248,3	K562	blood:
18	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
19	chr21:40755802..40758273-chr21:40758369..40760779,2	MCF-7	breast:
20	chr21:40759594..40762847-chr21:40822621..40825193,3	K562	blood:
21	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:
22	21:40687235-40690033..21:40757151-40764378	K562	blood:
23	chr21:40750392..40754801-chr21:40757428..40762186,12	MCF-7	breast:
24	chr21:40748679..40750675-chr21:40758576..40761248,3	K562	blood:
25	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
26	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
27	21:40686083-40686932..21:40757151-40764378	K562	blood:
28	chr21:40758008..40760801-chr21:40816074..40819285,3	MCF-7	breast:
29	chr21:40758092..40760884-chr21:40816362..40818206,3	K562	blood:
30	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
31	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
32	chr21:40750891..40755008-chr21:40755976..40761346,13	MCF-7	breast:
33	chr21:40759292..40761069-chr21:40781933..40784921,2	MCF-7	breast:

No data

Variant related genes	Relation type
WRB	TF binding region
ENSG00000238556	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000238141	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1060180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775662	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701047	0.82[EUR][1000 genomes]
rs13051571	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13051949	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094874	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2244352	0.81[ASN][1000 genomes]
rs2299739	0.83[EUR][1000 genomes]
rs2299741	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836992	0.81[YRI][hapmap]
rs2836994	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs2836995	0.92[CHB][hapmap]
rs2836996	0.93[CHB][hapmap]
rs2836997	0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837000	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837001	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837002	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837003	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2837004	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2837005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837008	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787923	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787924	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816624	0.93[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4818035	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517547	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8131718	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305674	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1056452	chr21:40741893-40782587	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2836998	WRB	cis	Artery Aorta	GTEx
rs2836998	WRB	cis	lung	GTEx
rs2836998	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs2836998	WRB	cis	Nerve Tibial	GTEx
rs2836998	LCA5L	cis	Esophagus Muscularis	GTEx
rs2836998	LCA5L	cis	Thyroid	GTEx
rs2836998	LCA5L	cis	Artery Tibial	GTEx
rs2836998	LCA5L	cis	Esophagus Mucosa	GTEx
rs2836998	LCA5L	cis	lung	GTEx
rs2836998	LCA5L	cis	Artery Aorta	GTEx
rs2836998	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2836998	LCA5L	cis	Heart Left Ventricle	GTEx
rs2836998	WRB	cis	Esophagus Mucosa	GTEx
rs2836998	LCA5L	cis	Whole Blood	GTEx
rs2836998	LCA5L	cis	Stomach	GTEx
rs2836998	WRB	cis	Esophagus Muscularis	GTEx
rs2836998	WRB	cis	Artery Tibial	GTEx
rs2836998	WRB	cis	Thyroid	GTEx
rs2836998	LCA5L	cis	Nerve Tibial	GTEx
rs2836998	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2836998	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2836998	WRB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40753400-40760200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40757400-40760200	Active TSS	Brain Anterior Caudate	brain
3	chr21:40758600-40760000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr21:40758600-40760000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr21:40758600-40760200	Active TSS	HSMM	muscle
6	chr21:40758600-40760600	Enhancers	Small Intestine	intestine
7	chr21:40758800-40760200	Active TSS	Gastric	stomach
8	chr21:40759000-40760000	Active TSS	Hela-S3	cervix
9	chr21:40759200-40760000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr21:40759200-40760000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:40759200-40760000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr21:40759200-40760000	Active TSS	Brain Angular Gyrus	brain
13	chr21:40759200-40760000	Active TSS	Fetal Stomach	stomach
14	chr21:40759200-40760000	Active TSS	Stomach Smooth Muscle	stomach
15	chr21:40759200-40760200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr21:40759200-40760200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr21:40759200-40760200	Active TSS	Fetal Intestine Small	intestine
18	chr21:40759200-40760200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr21:40759200-40760200	Active TSS	HMEC	breast
20	chr21:40759200-40760200	Active TSS	HSMMtube	muscle
21	chr21:40759200-40760200	Active TSS	K562	blood
22	chr21:40759200-40760200	Active TSS	NHDF-Ad	bronchial
23	chr21:40759200-40760400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr21:40759200-40760600	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr21:40759200-40760600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr21:40759200-40761000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr21:40759400-40760000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr21:40759400-40760000	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr21:40759400-40760000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr21:40759400-40760000	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr21:40759400-40760000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr21:40759400-40760000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr21:40759400-40760000	Active TSS	Liver	Liver
34	chr21:40759400-40760000	Active TSS	Brain Cingulate Gyrus	brain
35	chr21:40759400-40760000	Active TSS	Brain Hippocampus Middle	brain
36	chr21:40759400-40760000	Active TSS	Duodenum Mucosa	Duodenum
37	chr21:40759400-40760000	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr21:40759400-40760000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr21:40759400-40760000	Active TSS	Fetal Lung	lung
40	chr21:40759400-40760000	Active TSS	Fetal Muscle Trunk	muscle
41	chr21:40759400-40760000	Active TSS	Placenta	Placenta
42	chr21:40759400-40760000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr21:40759400-40760000	Active TSS	HepG2	liver
44	chr21:40759400-40760000	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr21:40759400-40760000	Active TSS	NHEK	skin
46	chr21:40759400-40760200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr21:40759400-40760200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr21:40759400-40760200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr21:40759400-40760200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr21:40759400-40760200	Active TSS	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links