Variant report

Variant	rs2837009
Chromosome Location	chr21:40779232-40779233
allele	C/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40777765..40780368-chr21:40791963..40794618,2	K562	blood:
2	chr21:40777120..40780319-chr21:40780700..40784709,5	K562	blood:
3	chr21:40777765..40781068-chr21:40793118..40796419,3	K562	blood:
4	chr21:40774564..40776388-chr21:40778753..40780258,2	K562	blood:
5	chr21:40758304..40761362-chr21:40776141..40780048,3	MCF-7	breast:
6	chr21:40778285..40779964-chr21:40794919..40796491,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGR-2	chr21:40778283-40781266	NONHSAT082186

No data

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11575939	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16997618	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2065313	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2205200	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2205201	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2223028	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2246078	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2410128	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837015	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837017	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837018	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2837019	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837020	1.00[JPT][hapmap]
rs2837021	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837022	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2837023	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837024	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837025	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837026	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837029	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837030	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837031	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837032	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837034	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837036	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837037	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837039	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837040	0.93[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2840267	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4281987	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56812456	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56866897	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58265345	0.89[ASN][1000 genomes]
rs58900137	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs596289	1.00[JPT][hapmap]
rs61342945	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7275686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276575	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276981	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7277627	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7279753	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73365952	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73367928	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367958	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367962	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367974	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367976	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73906032	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906033	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906034	1.00[ASN][1000 genomes]
rs940625	1.00[JPT][hapmap]
rs9680443	0.84[EUR][1000 genomes];0.81[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2837009	WRB	cis	lung	GTEx
rs2837009	WRB	cis	Adipose Subcutaneous	GTEx
rs2837009	LCA5L	cis	Thyroid	GTEx
rs2837009	LCA5L	cis	Nerve Tibial	GTEx
rs2837009	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs2837009	WRB	cis	Nerve Tibial	GTEx
rs2837009	LCA5L	cis	lung	GTEx
rs2837009	LCA5L	cis	Artery Tibial	GTEx
rs2837009	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837009	WRB	cis	Artery Tibial	GTEx
rs2837009	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2837009	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40761000-40782600	Weak transcription	Right Atrium	heart
2	chr21:40764600-40800600	Weak transcription	Psoas Muscle	Psoas
3	chr21:40765200-40780400	Weak transcription	Stomach Mucosa	stomach
4	chr21:40765400-40780000	Weak transcription	A549	lung
5	chr21:40765600-40781200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:40766800-40783400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr21:40767200-40779400	Weak transcription	Hela-S3	cervix
8	chr21:40767200-40781000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr21:40768000-40779800	Weak transcription	Placenta	Placenta
10	chr21:40768200-40781400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr21:40768200-40784600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr21:40768800-40782200	Weak transcription	Fetal Thymus	thymus
13	chr21:40769000-40779400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr21:40769000-40780000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr21:40769400-40783200	Weak transcription	Primary B cells from cord blood	blood
16	chr21:40770200-40785800	Weak transcription	Esophagus	oesophagus
17	chr21:40770400-40779800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr21:40770400-40780600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr21:40772600-40786400	Weak transcription	Fetal Heart	heart
20	chr21:40776600-40786200	Weak transcription	K562	blood
21	chr21:40777200-40780200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr21:40777600-40780000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr21:40777600-40780800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr21:40777600-40781000	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr21:40777800-40780400	Strong transcription	Brain Hippocampus Middle	brain
26	chr21:40777800-40780400	Strong transcription	Fetal Intestine Large	intestine
27	chr21:40777800-40780600	Strong transcription	Adipose Nuclei	Adipose
28	chr21:40777800-40780600	Strong transcription	Liver	Liver
29	chr21:40777800-40780600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr21:40777800-40781200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr21:40778000-40779400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr21:40778000-40780600	Strong transcription	Brain Angular Gyrus	brain
33	chr21:40778000-40780600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr21:40778000-40781400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr21:40778200-40779800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr21:40778200-40780400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:40778200-40780400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr21:40778200-40780600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr21:40778200-40780600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr21:40778200-40780800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr21:40778200-40780800	Strong transcription	Dnd41	blood
42	chr21:40778200-40781400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr21:40778200-40783800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
45	chr21:40778400-40779800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr21:40778400-40779800	Weak transcription	Aorta	Aorta
47	chr21:40778400-40779800	Weak transcription	Thymus	Thymus
48	chr21:40778400-40779800	Weak transcription	HSMMtube	muscle
49	chr21:40778400-40780000	Strong transcription	Fetal Lung	lung
50	chr21:40778400-40780200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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