Variant report

Variant	rs11601316
Chromosome Location	chr11:9536866-9536867
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9534694..9537562-chr11:9542413..9544187,2	MCF-7	breast:
2	chr11:9482189..9484807-chr11:9536719..9538236,2	K562	blood:

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1020621	0.95[JPT][hapmap]
rs1020622	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10770028	0.95[JPT][hapmap]
rs10770032	0.95[JPT][hapmap]
rs10770034	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10770037	0.90[CHD][hapmap]
rs10840228	0.95[JPT][hapmap]
rs10840234	0.89[JPT][hapmap]
rs10840235	0.89[JPT][hapmap]
rs10840243	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10840244	0.83[ASN][1000 genomes]
rs10840245	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840247	0.92[ASN][1000 genomes]
rs10840249	0.94[ASN][1000 genomes]
rs10840253	0.85[CEU][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs11042328	0.95[JPT][hapmap]
rs11042329	0.85[JPT][hapmap]
rs11042353	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042355	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042356	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042366	0.95[JPT][hapmap]
rs11042374	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042377	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11042393	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042395	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042397	0.95[EUR][1000 genomes]
rs12792161	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12795344	0.95[JPT][hapmap]
rs12806418	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1377667	0.95[ASN][1000 genomes]
rs1470895	0.92[ASN][1000 genomes]
rs1470896	0.95[ASN][1000 genomes]
rs1543	0.95[ASN][1000 genomes]
rs17258462	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1968717	0.91[ASN][1000 genomes]
rs2278900	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2290423	0.90[JPT][hapmap]
rs2290424	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290425	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35781320	0.81[EUR][1000 genomes]
rs3763874	0.89[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3763877	0.95[ASN][1000 genomes]
rs41369549	0.92[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.92[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4910053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910468	0.95[ASN][1000 genomes]
rs4910472	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6486307	0.95[JPT][hapmap]
rs6486359	0.81[EUR][1000 genomes]
rs6486361	0.95[JPT][hapmap]
rs6486394	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67548305	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7102473	0.91[ASN][1000 genomes]
rs7103931	0.82[EUR][1000 genomes]
rs7104568	0.96[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7122252	0.95[JPT][hapmap]
rs723297	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs727405	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs729313	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7395411	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7483667	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7926589	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7927350	0.90[JPT][hapmap]
rs7928945	0.81[AMR][1000 genomes]
rs7932192	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7933621	0.91[ASN][1000 genomes]
rs7938998	0.94[EUR][1000 genomes]
rs7939724	0.90[CHD][hapmap]
rs7944435	0.82[EUR][1000 genomes]
rs7944578	0.90[JPT][hapmap]
rs7949973	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8785	0.94[JPT][hapmap]
rs972594	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11601316	SNORA23	cis	cerebellum	SCAN

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	chr11:9521000-9545200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:9523400-9550800	Weak transcription	Colonic Mucosa	Colon
5	chr11:9523400-9551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:9528000-9540000	Strong transcription	Fetal Thymus	thymus
7	chr11:9528800-9550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:9529200-9550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:9530000-9541000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:9530200-9538400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:9530200-9538800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:9530200-9539600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:9530200-9540000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:9530200-9540200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr11:9530200-9541400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:9530200-9541400	Strong transcription	Adipose Nuclei	Adipose
17	chr11:9530200-9544600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:9530200-9551000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr11:9530400-9539400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:9531000-9550800	Weak transcription	Pancreas	Pancrea
21	chr11:9531600-9539600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:9532600-9546400	Weak transcription	Stomach Mucosa	stomach
23	chr11:9533400-9541600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:9533400-9550600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:9533600-9537600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:9533600-9538400	Strong transcription	Colon Smooth Muscle	Colon
27	chr11:9533600-9538400	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:9533600-9539200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:9533600-9539200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:9533600-9539800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:9533600-9539800	Strong transcription	Fetal Lung	lung
32	chr11:9533600-9540000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:9533600-9540000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:9533600-9540000	Strong transcription	K562	blood
35	chr11:9533600-9541200	Strong transcription	Primary B cells from cord blood	blood
36	chr11:9533600-9541400	Strong transcription	Primary T cells from cord blood	blood
37	chr11:9533800-9539000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:9533800-9540200	Strong transcription	GM12878-XiMat	blood
39	chr11:9534000-9537800	Strong transcription	Lung	lung
40	chr11:9534000-9538000	Strong transcription	Thymus	Thymus
41	chr11:9534000-9538200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr11:9534000-9538200	Strong transcription	Brain Hippocampus Middle	brain
43	chr11:9534000-9538800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:9534000-9538800	Strong transcription	Fetal Stomach	stomach
45	chr11:9534000-9539000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr11:9534000-9539000	Strong transcription	Brain Germinal Matrix	brain
47	chr11:9534000-9539200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:9534000-9539200	Strong transcription	Fetal Muscle Leg	muscle
49	chr11:9534000-9539200	Strong transcription	Left Ventricle	heart
50	chr11:9534000-9539200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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