Variant report

Variant	rs2278900
Chromosome Location	chr11:9495961-9495962
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9479692..9486524-chr11:9491765..9498081,14	K562	blood:

Variant related genes	Relation type
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1020621	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1020622	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10770028	0.95[JPT][hapmap]
rs10770032	0.95[JPT][hapmap]
rs10770033	0.85[ASN][1000 genomes]
rs10770034	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10770037	0.89[CHD][hapmap];0.83[MEX][hapmap]
rs10840228	0.95[JPT][hapmap]
rs10840234	0.89[JPT][hapmap]
rs10840235	0.90[JPT][hapmap]
rs10840237	0.83[ASN][1000 genomes]
rs10840238	0.84[ASN][1000 genomes]
rs10840243	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs10840244	0.91[ASN][1000 genomes]
rs10840245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840247	1.00[ASN][1000 genomes]
rs10840249	0.95[ASN][1000 genomes]
rs10840253	0.85[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs11042328	0.95[JPT][hapmap]
rs11042329	0.85[JPT][hapmap]
rs11042348	0.82[ASN][1000 genomes]
rs11042350	0.84[ASN][1000 genomes]
rs11042353	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042355	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042356	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042366	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11042374	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042377	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042393	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042397	0.88[EUR][1000 genomes]
rs11601316	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11826606	0.86[EUR][1000 genomes]
rs12271897	0.84[ASN][1000 genomes]
rs12282176	0.85[ASN][1000 genomes]
rs12296039	0.81[ASN][1000 genomes]
rs12792161	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12795344	0.95[JPT][hapmap]
rs12797567	0.82[ASN][1000 genomes]
rs12800802	0.84[ASN][1000 genomes]
rs12806418	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1377667	0.97[ASN][1000 genomes]
rs1470895	0.94[ASN][1000 genomes]
rs1470896	0.97[ASN][1000 genomes]
rs1543	0.97[ASN][1000 genomes]
rs17258462	0.80[AMR][1000 genomes]
rs1901919	0.81[YRI][hapmap]
rs1968717	0.98[ASN][1000 genomes]
rs2290423	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2290424	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290425	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35781320	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3763874	0.89[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3763877	0.97[ASN][1000 genomes]
rs41369549	0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910053	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910468	0.97[ASN][1000 genomes]
rs6486307	0.95[JPT][hapmap]
rs6486359	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6486361	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6486394	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs67548305	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7101776	0.82[YRI][hapmap]
rs7102473	0.98[ASN][1000 genomes]
rs7103931	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7104568	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7122252	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs723297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs727405	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs729313	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7395411	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7483667	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7926589	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs7927350	0.90[JPT][hapmap]
rs7928823	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7928945	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7932192	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7933621	0.98[ASN][1000 genomes]
rs7938998	0.90[EUR][1000 genomes]
rs7939388	0.82[YRI][hapmap]
rs7939724	0.90[CHD][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap]
rs7944435	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7944578	0.90[JPT][hapmap]
rs7949973	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8785	0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs972594	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[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	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2278900	SNORA23	cis	cerebellum	SCAN
rs2278900	IPO7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9483400-9499800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:9483600-9499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:9483600-9499400	Weak transcription	Pancreas	Pancrea
4	chr11:9483600-9518600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:9484000-9499600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:9484200-9499800	Weak transcription	Brain Angular Gyrus	brain
7	chr11:9484600-9544800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:9484800-9496000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:9485200-9520000	Weak transcription	Stomach Mucosa	stomach
10	chr11:9485400-9499600	Weak transcription	A549	lung
11	chr11:9485600-9499800	Weak transcription	Hela-S3	cervix
12	chr11:9489600-9524000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr11:9489800-9523400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr11:9490800-9497800	Strong transcription	Primary T cells from cord blood	blood
15	chr11:9491200-9497800	Strong transcription	Primary B cells from cord blood	blood
16	chr11:9491200-9497800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr11:9491400-9496800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:9491400-9498200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr11:9491400-9506200	Strong transcription	Liver	Liver
20	chr11:9491400-9525400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:9491600-9497400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:9491600-9497800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr11:9491600-9497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:9491600-9497800	Strong transcription	Fetal Muscle Leg	muscle
26	chr11:9491600-9497800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:9491600-9498200	Strong transcription	Fetal Lung	lung
28	chr11:9491600-9502600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:9492000-9496400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr11:9492000-9498200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:9492000-9498200	Strong transcription	Left Ventricle	heart
32	chr11:9492000-9506000	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr11:9492000-9527200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:9492200-9497000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:9492200-9497800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:9492200-9497800	Strong transcription	Adipose Nuclei	Adipose
37	chr11:9492200-9503000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:9492200-9525400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:9492400-9497200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:9492600-9498800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:9492600-9502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:9492600-9505800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr11:9492800-9496200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:9492800-9496800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:9492800-9497600	Strong transcription	Fetal Intestine Large	intestine
46	chr11:9492800-9497800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:9492800-9498400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:9492800-9498400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr11:9492800-9499600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr11:9492800-9507800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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