Variant report

Variant	rs2290423
Chromosome Location	chr11:9450377-9450378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9447701..9450572-chr11:9481621..9483172,2	MCF-7	breast:
2	chr11:9443893..9446629-chr11:9448948..9451710,3	MCF-7	breast:
3	chr11:9445134..9447158-chr11:9449371..9452309,2	K562	blood:

Variant related genes	Relation type
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000205339	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1020621	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1020622	0.95[ASN][1000 genomes]
rs10743107	0.87[ASN][1000 genomes]
rs10770028	0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10770029	0.86[ASN][1000 genomes]
rs10770032	0.88[ASW][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10770033	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10770037	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs10840228	0.87[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10840234	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10840235	0.84[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10840236	0.90[ASN][1000 genomes]
rs10840237	0.95[ASN][1000 genomes]
rs10840238	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840241	0.82[ASN][1000 genomes]
rs10840243	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840245	0.90[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs10840247	0.81[ASN][1000 genomes]
rs10840253	0.82[JPT][hapmap]
rs11042328	0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11042329	0.87[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11042348	0.94[ASN][1000 genomes]
rs11042349	0.91[ASN][1000 genomes]
rs11042350	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042353	0.95[ASN][1000 genomes]
rs11042355	0.95[ASN][1000 genomes]
rs11042356	0.95[ASN][1000 genomes]
rs11042366	1.00[CEU][hapmap];0.80[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042377	0.82[ASN][1000 genomes]
rs11042395	0.90[JPT][hapmap]
rs11826606	0.90[ASN][1000 genomes]
rs12225755	0.90[ASN][1000 genomes]
rs12271897	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12282176	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12296039	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12792161	0.81[ASN][1000 genomes]
rs12795344	0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12797567	0.94[ASN][1000 genomes]
rs12799672	0.83[ASN][1000 genomes]
rs12800802	0.94[ASN][1000 genomes]
rs12806418	0.81[ASN][1000 genomes]
rs1968717	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278900	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2290424	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs2290425	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs35781320	0.92[ASN][1000 genomes]
rs3763873	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs41369549	0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4910048	0.91[GIH][hapmap]
rs4910053	0.90[JPT][hapmap]
rs6486306	0.83[ASN][1000 genomes]
rs6486307	0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs6486359	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6486361	0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6486394	0.90[JPT][hapmap]
rs67548305	0.95[ASN][1000 genomes]
rs7102473	0.82[ASN][1000 genomes]
rs7103931	0.89[ASN][1000 genomes]
rs7104568	0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs7114824	0.89[ASN][1000 genomes]
rs7115477	0.83[GIH][hapmap]
rs7122252	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7122499	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs723297	0.90[JPT][hapmap]
rs727405	0.92[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs729313	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7395411	0.93[ASN][1000 genomes]
rs7480643	0.81[GIH][hapmap]
rs7926589	0.96[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs7927350	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7928823	0.81[ASN][1000 genomes]
rs7928945	0.83[ASN][1000 genomes]
rs7932192	0.85[ASN][1000 genomes]
rs7933621	0.82[ASN][1000 genomes]
rs7939724	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs7944435	0.86[ASN][1000 genomes]
rs7944578	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7949973	0.95[ASN][1000 genomes]
rs8785	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9667574	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs972594	0.90[JPT][hapmap]

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	nsv982982	chr11:9450348-9452590	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2290423	SNORA23	cis	parietal	SCAN
rs2290423	SNORA23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9407600-9464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:9416000-9456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:9419600-9471000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:9420600-9450400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:9421000-9471200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:9423000-9470400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:9424200-9470400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:9424800-9468600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:9424800-9469000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:9424800-9470600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:9425000-9468200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:9425000-9468400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr11:9425200-9467200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:9425800-9468000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:9426200-9471600	Strong transcription	Dnd41	blood
16	chr11:9426800-9468400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr11:9426800-9470600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:9427200-9466800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:9427600-9471000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:9429800-9469000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:9430200-9459600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:9430200-9470200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:9430400-9457400	Strong transcription	A549	lung
24	chr11:9430400-9468200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:9431000-9453000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr11:9431800-9468800	Weak transcription	Stomach Mucosa	stomach
27	chr11:9432800-9450400	Weak transcription	Spleen	Spleen
28	chr11:9433000-9464000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr11:9433200-9451400	Weak transcription	Aorta	Aorta
30	chr11:9434800-9470400	Strong transcription	Osteobl	bone
31	chr11:9435400-9466600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr11:9435400-9470400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:9436800-9450600	Weak transcription	Esophagus	oesophagus
34	chr11:9439400-9468200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:9439600-9467600	Strong transcription	Placenta	Placenta
36	chr11:9439600-9468000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:9439600-9472000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:9439800-9467000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:9439800-9468200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:9439800-9470200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:9439800-9470600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:9440000-9452800	Strong transcription	Adipose Nuclei	Adipose
43	chr11:9440000-9465600	Strong transcription	NH-A	brain
44	chr11:9440000-9466200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:9440000-9470800	Strong transcription	Fetal Thymus	thymus
46	chr11:9440200-9466600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:9440200-9468200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr11:9440200-9468400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr11:9440200-9470400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr11:9441600-9466800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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