Variant report

Variant	rs7927350
Chromosome Location	chr11:9476419-9476420
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	chr11:9475198..9478964-chr11:9479689..9482782,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1020621	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1020622	0.85[ASN][1000 genomes]
rs10770028	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10770032	0.88[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[YRI][hapmap]
rs10770033	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10770037	0.84[CEU][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap]
rs10840228	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10840234	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs10840235	0.83[GIH][hapmap];0.89[JPT][hapmap]
rs10840236	0.80[ASN][1000 genomes]
rs10840237	0.85[ASN][1000 genomes]
rs10840238	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840243	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10840244	0.82[EUR][1000 genomes]
rs10840245	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs10840253	0.81[JPT][hapmap]
rs11042328	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11042329	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs11042348	0.84[ASN][1000 genomes]
rs11042349	0.82[ASN][1000 genomes]
rs11042350	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042353	0.85[ASN][1000 genomes]
rs11042355	0.85[ASN][1000 genomes]
rs11042356	0.85[ASN][1000 genomes]
rs11042366	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042395	0.90[JPT][hapmap]
rs11826606	0.80[ASN][1000 genomes]
rs12225755	0.81[ASN][1000 genomes]
rs12271897	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12282176	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12296039	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12795344	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs12797567	0.84[ASN][1000 genomes]
rs12800802	0.84[ASN][1000 genomes]
rs1968717	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2278900	0.90[JPT][hapmap]
rs2290423	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]
rs2290424	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs2290425	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs35781320	0.84[ASN][1000 genomes]
rs3763873	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs3763877	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs41369549	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4910048	0.91[GIH][hapmap]
rs4910053	0.90[JPT][hapmap]
rs6486307	0.94[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs6486359	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6486361	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6486394	0.90[JPT][hapmap]
rs67548305	0.85[ASN][1000 genomes]
rs7103931	0.93[ASN][1000 genomes]
rs7104568	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[ASN][1000 genomes]
rs7115477	0.83[GIH][hapmap]
rs7122252	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7122499	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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]
rs7395411	0.85[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[MKK][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs7928823	0.88[ASN][1000 genomes]
rs7928945	0.89[ASN][1000 genomes]
rs7932192	0.91[ASN][1000 genomes]
rs7939724	0.84[CEU][hapmap];0.88[MEX][hapmap]
rs7944435	0.96[ASN][1000 genomes]
rs7944578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7949973	0.85[ASN][1000 genomes]
rs8785	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9667574	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs972594	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv825762	chr11:9470175-9479714	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7927350	SNORA23	cis	cerebellum	SCAN
rs7927350	SNORA23	cis	parietal	SCAN
rs7927350	IPO7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9452800-9480000	Weak transcription	Fetal Brain Male	brain
2	chr11:9457800-9480600	Weak transcription	Psoas Muscle	Psoas
3	chr11:9462200-9481000	Weak transcription	NHLF	lung
4	chr11:9463400-9481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:9463800-9481000	Weak transcription	NHDF-Ad	bronchial
6	chr11:9464800-9480800	Weak transcription	HSMMtube	muscle
7	chr11:9465000-9480800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:9465000-9480800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:9465000-9481000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:9465200-9481000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:9465200-9481200	Weak transcription	Ovary	ovary
12	chr11:9465400-9481000	Weak transcription	Brain Substantia Nigra	brain
13	chr11:9465400-9481000	Weak transcription	K562	blood
14	chr11:9465800-9480600	Weak transcription	Esophagus	oesophagus
15	chr11:9465800-9481000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr11:9466400-9480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:9466600-9480800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr11:9466800-9480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:9466800-9481000	Weak transcription	Fetal Lung	lung
20	chr11:9467000-9480800	Weak transcription	Lung	lung
21	chr11:9467400-9480800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:9468000-9481000	Weak transcription	Fetal Heart	heart
23	chr11:9468000-9481000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:9468000-9481000	Weak transcription	NH-A	brain
25	chr11:9468200-9481000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:9470200-9480800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr11:9470200-9480800	Weak transcription	Left Ventricle	heart
28	chr11:9470200-9480800	Weak transcription	HSMM	muscle
29	chr11:9470200-9480800	Weak transcription	NHEK	skin
30	chr11:9470200-9481000	Weak transcription	A549	lung
31	chr11:9470200-9481000	Weak transcription	HUVEC	blood vessel
32	chr11:9470200-9481200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:9470400-9480800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:9470400-9480800	Weak transcription	HMEC	breast
35	chr11:9470400-9481000	Weak transcription	Osteobl	bone
36	chr11:9470600-9480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:9470800-9480800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:9471000-9480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:9471000-9480800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:9471600-9480200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:9472000-9480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:9473200-9480800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:9473600-9480800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:9473800-9480600	Weak transcription	Brain Germinal Matrix	brain
45	chr11:9473800-9480800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr11:9474000-9480800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:9474000-9480800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:9474000-9480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:9474000-9481000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:9475200-9481200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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