Variant report

Variant	rs10210840
Chromosome Location	chr2:55226009-55226010
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55224744..55226462-chr2:55275391..55278252,2	K562	blood:
2	chr2:55224682..55227904-chr2:55233478..55236485,4	MCF-7	breast:
3	chr2:55224190..55226193-chr2:55238312..55240025,2	K562	blood:
4	chr2:55224711..55226341-chr2:55275283..55277767,2	MCF-7	breast:
5	chr2:55224254..55226682-chr2:55399758..55402693,2	K562	blood:
6	chr2:55223597..55226125-chr2:55260747..55262677,2	K562	blood:
7	chr2:55224031..55227614-chr2:55234894..55236977,3	K562	blood:
8	chr2:55221662..55224053-chr2:55225919..55227544,2	MCF-7	breast:
9	chr2:55194049..55196977-chr2:55224979..55226629,2	K562	blood:
10	chr2:55225943..55228351-chr2:55458168..55460994,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000214595	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10174838	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10189379	0.85[YRI][hapmap]
rs11674808	0.83[EUR][1000 genomes]
rs12464070	0.87[ASN][1000 genomes]
rs12477711	0.90[ASN][1000 genomes]
rs12713284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13011689	0.84[EUR][1000 genomes]
rs13387751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2015919	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044291	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255112	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255393	0.91[JPT][hapmap]
rs2580764	0.83[ASN][1000 genomes]
rs2580765	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2580772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2580773	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2580776	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2588510	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2588514	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2588517	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2588518	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2588519	0.86[JPT][hapmap]
rs2588521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2860453	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2902649	0.90[ASN][1000 genomes]
rs2919129	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920878	0.96[CEU][hapmap]
rs2920893	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2920900	0.83[EUR][1000 genomes]
rs2968786	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968787	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2968790	0.82[EUR][1000 genomes]
rs2968793	0.84[EUR][1000 genomes]
rs2968794	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2968795	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2968804	0.87[JPT][hapmap]
rs2972072	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2972075	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2972090	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2972097	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35631428	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35826668	0.93[ASN][1000 genomes]
rs3806570	0.92[ASN][1000 genomes]
rs4672005	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545466	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726158	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6755468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6760429	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7340476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7562292	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570629	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7584430	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7601625	0.82[YRI][hapmap]
rs968998	1.00[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10210840	RTN4	cis	Esophagus Muscularis	GTEx
rs10210840	RTN4	cis	Whole Blood	GTEx
rs10210840	RTN4	cis	Nerve Tibial	GTEx
rs10210840	RTN4	cis	Artery Tibial	GTEx
rs10210840	RTN4	cis	Adipose Subcutaneous	GTEx
rs10210840	RTN4	cis	Artery Aorta	GTEx
rs10210840	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs10210840	RTN4	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
3	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
5	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
8	chr2:55213800-55226400	Weak transcription	Ovary	ovary
9	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
11	chr2:55214800-55226400	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:55214800-55226400	Weak transcription	Fetal Thymus	thymus
13	chr2:55214800-55227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:55214800-55227200	Weak transcription	HepG2	liver
15	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
16	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:55215200-55227200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:55215200-55234200	Weak transcription	Dnd41	blood
22	chr2:55216200-55226400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:55216400-55226400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:55217200-55226400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:55217200-55226400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:55219400-55228800	Weak transcription	Aorta	Aorta
27	chr2:55219400-55233400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:55220000-55226600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:55220200-55227000	Enhancers	Brain Angular Gyrus	brain
30	chr2:55220400-55236800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:55221000-55226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:55221000-55226400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:55222800-55226200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:55222800-55226400	Enhancers	Colon Smooth Muscle	Colon
35	chr2:55222800-55226400	Genic enhancers	HSMM	muscle
36	chr2:55222800-55227800	Enhancers	Brain Substantia Nigra	brain
37	chr2:55222800-55228000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr2:55222800-55228600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:55222800-55229000	Enhancers	Brain Anterior Caudate	brain
40	chr2:55223000-55226600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:55223000-55237200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:55223200-55227400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:55223400-55226400	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr2:55224400-55226600	Enhancers	Primary hematopoietic stem cells	blood
45	chr2:55224400-55226600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr2:55224400-55227800	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:55224400-55228000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr2:55224400-55228800	Enhancers	Adipose Nuclei	Adipose
49	chr2:55224600-55226200	Enhancers	Osteobl	bone
50	chr2:55224600-55227600	Enhancers	Primary T cells from cord blood	blood

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