Variant report

Variant	rs2290424
Chromosome Location	chr11:9533701-9533702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9480637..9483121-chr11:9531195..9534021,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1020621	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1020622	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10770028	0.95[JPT][hapmap]
rs10770032	0.95[JPT][hapmap]
rs10770033	0.81[ASN][1000 genomes]
rs10770034	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10770037	0.90[CHD][hapmap];0.84[MEX][hapmap]
rs10840228	0.95[JPT][hapmap]
rs10840234	0.89[JPT][hapmap]
rs10840235	0.90[JPT][hapmap]
rs10840243	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs10840244	0.86[ASN][1000 genomes]
rs10840245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840247	0.95[ASN][1000 genomes]
rs10840249	0.97[ASN][1000 genomes]
rs10840253	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs11042328	0.95[JPT][hapmap]
rs11042329	0.85[JPT][hapmap]
rs11042353	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042355	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042356	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042366	0.95[JPT][hapmap];0.80[MEX][hapmap]
rs11042374	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042377	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042393	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042397	0.96[EUR][1000 genomes]
rs11601316	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12282176	0.81[ASN][1000 genomes]
rs12792161	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12795344	0.95[JPT][hapmap]
rs12806418	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1377667	0.98[ASN][1000 genomes]
rs1470895	0.95[ASN][1000 genomes]
rs1470896	0.98[ASN][1000 genomes]
rs1543	0.98[ASN][1000 genomes]
rs17258462	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1968717	0.94[ASN][1000 genomes]
rs2278900	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]
rs2290423	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs2290425	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];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35781320	0.81[EUR][1000 genomes]
rs3763874	0.92[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3763877	0.98[ASN][1000 genomes]
rs41369549	0.89[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.89[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910053	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910468	0.98[ASN][1000 genomes]
rs4910472	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6486307	0.95[JPT][hapmap]
rs6486359	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6486361	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6486394	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs67548305	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7102473	0.94[ASN][1000 genomes]
rs7103931	0.82[EUR][1000 genomes]
rs7104568	0.92[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs7122252	0.95[JPT][hapmap];0.80[MEX][hapmap]
rs723297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs727405	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs729313	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7395411	0.83[EUR][1000 genomes]
rs7483667	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7926589	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs7927350	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs7928945	0.80[AMR][1000 genomes]
rs7932192	0.81[EUR][1000 genomes]
rs7933621	0.94[ASN][1000 genomes]
rs7938998	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7939724	0.92[ASW][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7944435	0.82[EUR][1000 genomes]
rs7944578	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs7949973	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8785	0.95[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs972594	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[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	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
2	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
3	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
4	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2290424	SNORA23	cis	cerebellum	SCAN
rs2290424	IPO7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9484600-9544800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:9501800-9534000	Weak transcription	Psoas Muscle	Psoas
4	chr11:9518800-9534000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:9519200-9534200	Weak transcription	Fetal Brain Female	brain
6	chr11:9521000-9545200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:9523000-9534000	Weak transcription	HMEC	breast
8	chr11:9523400-9534000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:9523400-9534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:9523400-9534000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:9523400-9534000	Weak transcription	Aorta	Aorta
12	chr11:9523400-9534000	Weak transcription	Brain Angular Gyrus	brain
13	chr11:9523400-9534000	Weak transcription	Fetal Brain Male	brain
14	chr11:9523400-9534200	Weak transcription	Right Ventricle	heart
15	chr11:9523400-9550800	Weak transcription	Colonic Mucosa	Colon
16	chr11:9523400-9551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:9525400-9534000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:9528000-9534800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr11:9528000-9540000	Strong transcription	Fetal Thymus	thymus
20	chr11:9528800-9534000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:9528800-9534000	Weak transcription	Ovary	ovary
22	chr11:9528800-9534200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:9528800-9534200	Weak transcription	Hela-S3	cervix
24	chr11:9528800-9550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:9529200-9550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr11:9529600-9534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:9530000-9534000	Enhancers	Fetal Intestine Large	intestine
28	chr11:9530000-9541000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:9530200-9538400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:9530200-9538800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr11:9530200-9539600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:9530200-9540000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:9530200-9540200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr11:9530200-9541400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:9530200-9541400	Strong transcription	Adipose Nuclei	Adipose
36	chr11:9530200-9544600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:9530200-9551000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr11:9530400-9539400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:9530600-9534000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:9530600-9534000	Enhancers	HepG2	liver
41	chr11:9530800-9534000	Weak transcription	Gastric	stomach
42	chr11:9530800-9534000	Weak transcription	Left Ventricle	heart
43	chr11:9531000-9534000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:9531000-9534000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:9531000-9534000	Weak transcription	Esophagus	oesophagus
46	chr11:9531000-9534000	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:9531000-9534000	Weak transcription	Fetal Stomach	stomach
48	chr11:9531000-9534000	Weak transcription	Lung	lung
49	chr11:9531000-9534000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr11:9531000-9534000	Weak transcription	Rectal Smooth Muscle	rectum

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