Variant report

Variant	rs2837002
Chromosome Location	chr21:40763986-40763987
allele	G/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: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	chr21:40684582..40688018-chr21:40762846..40766549,4	MCF-7	breast:
2	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
3	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
4	chr21:40757591..40761225-chr21:40763023..40767191,7	K562	blood:
5	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:
6	21:40687235-40690033..21:40757151-40764378	K562	blood:
7	21:40686083-40686932..21:40757151-40764378	K562	blood:
8	chr21:40762468..40764445-chr21:40783033..40785602,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238141	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1060180	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775662	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701047	0.81[EUR][1000 genomes]
rs13051571	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13051949	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094874	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2244352	0.81[ASN][1000 genomes]
rs2299739	0.83[EUR][1000 genomes]
rs2299741	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836994	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs2836995	0.92[CHB][hapmap]
rs2836996	0.92[CHB][hapmap]
rs2836997	0.92[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836998	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]
rs2836999	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837000	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837001	0.96[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	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837006	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837007	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837008	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787923	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787924	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816624	0.92[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4818035	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818036	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517547	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8131718	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305674	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974828	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs2837002	LCA5L	cis	lung	GTEx
rs2837002	LCA5L	cis	Heart Left Ventricle	GTEx
rs2837002	LCA5L	cis	Artery Aorta	GTEx
rs2837002	WRB	cis	parietal	SCAN
rs2837002	WRB	cis	Whole Blood	GTEx
rs2837002	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837002	WRB	cis	Esophagus Mucosa	GTEx
rs2837002	LCA5L	cis	Nerve Tibial	GTEx
rs2837002	WRB	cis	Artery Aorta	GTEx
rs2837002	LCA5L	cis	Whole Blood	GTEx
rs2837002	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2837002	WRB	cis	lung	GTEx
rs2837002	LCA5L	cis	Thyroid	GTEx
rs2837002	LCA5L	cis	Stomach	GTEx
rs2837002	WRB	cis	Esophagus Muscularis	GTEx
rs2837002	WRB	cis	Nerve Tibial	GTEx
rs2837002	WRB	cis	Adipose Subcutaneous	GTEx
rs2837002	HMGN1	cis	lymphoblastoid	seeQTL
rs2837002	LCA5L	cis	Esophagus Muscularis	GTEx
rs2837002	LCA5L	cis	Artery Tibial	GTEx
rs2837002	HMGN1	cis	cerebellum	SCAN
rs2837002	WRB	cis	cerebellum	SCAN
rs2837002	WRB	cis	Thyroid	GTEx
rs2837002	WRB	cis	Artery Tibial	GTEx
rs2837002	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2837002	LCA5L	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40760600-40764000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:40760600-40764400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr21:40760600-40771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:40760800-40766400	Weak transcription	Fetal Kidney	kidney
5	chr21:40761000-40764000	Weak transcription	A549	lung
6	chr21:40761000-40764400	Weak transcription	Psoas Muscle	Psoas
7	chr21:40761000-40764600	Weak transcription	Fetal Brain Male	brain
8	chr21:40761000-40765000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr21:40761000-40769800	Weak transcription	HMEC	breast
10	chr21:40761000-40777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr21:40761000-40779200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr21:40761000-40782600	Weak transcription	Right Atrium	heart
13	chr21:40761200-40771200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr21:40761400-40764000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr21:40761600-40764200	Weak transcription	Stomach Mucosa	stomach
16	chr21:40761800-40768200	Strong transcription	Fetal Intestine Small	intestine
17	chr21:40762000-40765400	Strong transcription	Colonic Mucosa	Colon
18	chr21:40762000-40765400	Strong transcription	NHLF	lung
19	chr21:40762200-40768200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr21:40762200-40768800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr21:40762200-40770400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr21:40762200-40770400	Strong transcription	Fetal Muscle Leg	muscle
23	chr21:40762200-40770600	Strong transcription	Fetal Brain Female	brain
24	chr21:40762200-40771400	Strong transcription	Fetal Stomach	stomach
25	chr21:40762400-40765800	Strong transcription	HepG2	liver
26	chr21:40762400-40766000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr21:40762400-40768000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr21:40762400-40768000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr21:40762400-40768200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:40762400-40768400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr21:40762400-40768800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr21:40762400-40769000	Strong transcription	Primary T cells from cord blood	blood
33	chr21:40762400-40770200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr21:40762400-40770400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr21:40762400-40770400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr21:40762400-40770400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr21:40762400-40770400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr21:40762400-40770400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr21:40762400-40770400	Strong transcription	Ovary	ovary
40	chr21:40762400-40770400	Strong transcription	Thymus	Thymus
41	chr21:40762400-40771000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr21:40762400-40771200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr21:40762600-40765800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr21:40762600-40767000	Strong transcription	Brain Angular Gyrus	brain
45	chr21:40762600-40767000	Strong transcription	Brain Substantia Nigra	brain
46	chr21:40762600-40767200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr21:40762600-40767400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr21:40762600-40767800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr21:40762600-40767800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:40762600-40767800	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links