Variant report

Variant	rs2353369
Chromosome Location	chr11:17007220-17007221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17000932..17002613-chr11:17006244..17008801,2	MCF-7	breast:
2	chr11:16997178..16999092-chr11:17003135..17008712,4	MCF-7	breast:
3	chr11:16990664..16992333-chr11:17006870..17009444,2	MCF-7	breast:
4	chr11:17006921..17009898-chr11:17019659..17022087,3	MCF-7	breast:
5	chr11:16981957..16983634-chr11:17005634..17007658,3	MCF-7	breast:
6	chr11:17001912..17011357-chr11:17032509..17037700,15	MCF-7	breast:
7	chr11:17007115..17010774-chr11:17033404..17036243,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166689	Chromatin interaction
ENSG00000184669	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10734250	0.80[YRI][hapmap]
rs10741719	0.95[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap]
rs10741720	0.95[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs10766366	0.92[EUR][1000 genomes]
rs10766367	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10766370	0.92[YRI][hapmap]
rs10832707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832710	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10832712	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832713	0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10832721	0.92[YRI][hapmap]
rs11024101	0.82[ASN][1000 genomes]
rs11024102	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11024103	0.97[ASN][1000 genomes]
rs11529141	0.91[EUR][1000 genomes]
rs1468489	0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2302207	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34927905	0.81[ASN][1000 genomes]
rs4141194	0.81[ASN][1000 genomes]
rs4237715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237716	0.96[CEU][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes]
rs4351794	0.90[LWK][hapmap];0.82[YRI][hapmap]
rs4469869	0.91[EUR][1000 genomes]
rs4757468	0.92[EUR][1000 genomes]
rs4757470	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4757472	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4757473	0.96[CEU][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes]
rs4757474	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757475	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757476	0.91[EUR][1000 genomes]
rs4757482	1.00[YRI][hapmap]
rs4757484	0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs4757487	0.96[YRI][hapmap]
rs4757489	0.95[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs4757490	0.90[LWK][hapmap];0.82[YRI][hapmap]
rs6486332	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6486333	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486334	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486335	0.95[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6486341	0.96[YRI][hapmap]
rs7118307	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7122802	0.91[EUR][1000 genomes]
rs7123383	0.81[ASN][1000 genomes]
rs7127818	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7930890	0.81[AFR][1000 genomes]
rs7931025	1.00[YRI][hapmap]
rs7933984	0.95[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap]
rs7934567	0.91[EUR][1000 genomes]
rs7940499	0.92[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7944490	0.91[EUR][1000 genomes]
rs7947297	0.95[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv983149	chr11:17003386-17011615	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2353369	RNU14	cis	multi-tissue	Pritchard
rs2353369	INSC	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16992200-17007400	Weak transcription	Colonic Mucosa	Colon
2	chr11:16998000-17009000	Enhancers	Stomach Mucosa	stomach
3	chr11:16998000-17011800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:16998800-17007800	Genic enhancers	Fetal Intestine Small	intestine
5	chr11:17000600-17011800	Enhancers	Pancreas	Pancrea
6	chr11:17001400-17010600	Enhancers	Placenta	Placenta
7	chr11:17003000-17009800	Enhancers	Brain Substantia Nigra	brain
8	chr11:17003600-17007800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:17003600-17009800	Enhancers	Brain Anterior Caudate	brain
10	chr11:17004000-17007400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:17004000-17007600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:17004000-17008000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:17004000-17008200	Weak transcription	Adipose Nuclei	Adipose
14	chr11:17004000-17008200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:17004000-17008400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:17004200-17007600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:17004200-17007600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:17004200-17008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:17004200-17008000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:17004200-17011200	Weak transcription	Brain Germinal Matrix	brain
21	chr11:17004400-17007400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:17004400-17007600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:17004400-17007600	Weak transcription	GM12878-XiMat	blood
24	chr11:17004400-17007800	Weak transcription	Spleen	Spleen
25	chr11:17004600-17007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:17004800-17007400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:17004800-17008000	Weak transcription	Fetal Muscle Leg	muscle
28	chr11:17004800-17034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:17005000-17007600	Weak transcription	Right Atrium	heart
30	chr11:17005000-17009400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:17005400-17009000	Enhancers	Fetal Intestine Large	intestine
32	chr11:17005800-17012200	Enhancers	Gastric	stomach
33	chr11:17006000-17007400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr11:17006000-17008400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr11:17006000-17009800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr11:17006000-17010000	Enhancers	Fetal Heart	heart
37	chr11:17006200-17013200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:17006400-17007600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr11:17006400-17013400	Weak transcription	Fetal Stomach	stomach
40	chr11:17006400-17034000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:17006600-17008600	Enhancers	Lung	lung
42	chr11:17006600-17009400	Enhancers	Left Ventricle	heart
43	chr11:17006600-17010000	Enhancers	Liver	Liver
44	chr11:17006800-17007600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:17006800-17007600	Weak transcription	Esophagus	oesophagus
46	chr11:17006800-17008200	Enhancers	Fetal Lung	lung
47	chr11:17007000-17007400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:17007000-17007400	Weak transcription	Small Intestine	intestine
49	chr11:17007000-17007600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:17007000-17009400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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