Variant report

Variant	rs500161
Chromosome Location	chr11:65695438-65695439
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	chr11:65695024..65697839-chr11:65700291..65702313,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10160792	0.82[AMR][1000 genomes]
rs1058068	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1151523	0.83[GIH][hapmap];0.85[MEX][hapmap]
rs1204649	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12361552	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs12797319	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs1786175	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs470192	0.92[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs491973	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs503524	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs528736	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs538954	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs542332	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs550435	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.82[EUR][1000 genomes]
rs556643	0.92[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs55928757	0.80[EUR][1000 genomes]
rs574586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs589253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590318	0.86[EUR][1000 genomes]
rs593525	0.81[MEX][hapmap]
rs606978	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs613924	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs617791	0.85[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs61893932	0.85[EUR][1000 genomes]
rs632578	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs637571	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs642293	0.81[EUR][1000 genomes]
rs653236	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs653914	1.00[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs655744	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs660118	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs669371	0.85[GIH][hapmap];0.85[MEX][hapmap]
rs674363	0.81[EUR][1000 genomes]
rs677029	1.00[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs679581	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs683191	1.00[YRI][hapmap]
rs694156	0.82[EUR][1000 genomes]
rs7107912	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
6	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
9	esv3444925	chr11:65687425-65714023	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs500161	PCNXL3	cis	parietal	SCAN
rs500161	RAB1B	cis	cerebellum	SCAN
rs500161	FADS3	cis	parietal	SCAN
rs500161	EFEMP2	cis	cerebellum	SCAN
rs500161	SNX32	cis	cerebellum	SCAN
rs500161	LRRN4CL	cis	cerebellum	SCAN
rs500161	EIF1AD	cis	parietal	SCAN
rs500161	ZNF408	trans	parietal	SCAN
rs500161	SNX32	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65687800-65699800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:65688600-65699000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:65688800-65715000	Weak transcription	Right Atrium	heart
4	chr11:65690400-65699000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:65690400-65699400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:65690400-65699600	Weak transcription	NH-A	brain
7	chr11:65690400-65699800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:65690400-65702000	Weak transcription	Fetal Brain Male	brain
9	chr11:65690600-65695600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:65690600-65695600	Weak transcription	Lung	lung
11	chr11:65690600-65695600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:65690600-65696400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:65690600-65697800	Weak transcription	Gastric	stomach
14	chr11:65690600-65705000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:65690800-65701000	Weak transcription	Esophagus	oesophagus
16	chr11:65691000-65699600	Weak transcription	A549	lung
17	chr11:65691200-65695600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:65691200-65699800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:65691200-65700000	Weak transcription	Brain Anterior Caudate	brain
20	chr11:65691200-65708600	Weak transcription	HSMM	muscle
21	chr11:65691400-65696200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65692200-65698800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:65692600-65695600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:65692600-65699400	Weak transcription	Fetal Lung	lung
25	chr11:65692600-65701600	Weak transcription	NHLF	lung
26	chr11:65692800-65697800	Weak transcription	Fetal Intestine Small	intestine
27	chr11:65692800-65698800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:65692800-65699400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:65692800-65700200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:65693000-65699400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr11:65693200-65699400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:65693400-65697000	Weak transcription	Brain Germinal Matrix	brain
33	chr11:65693400-65699000	Weak transcription	Fetal Brain Female	brain
34	chr11:65693400-65699400	Weak transcription	Placenta	Placenta
35	chr11:65693600-65701600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr11:65694000-65695600	Weak transcription	Fetal Stomach	stomach
37	chr11:65694000-65696600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:65694000-65708200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:65694800-65696800	Enhancers	Spleen	Spleen
40	chr11:65695000-65695800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr11:65695000-65695800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:65695000-65696400	Enhancers	Colonic Mucosa	Colon
43	chr11:65695000-65696800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:65695200-65695600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr11:65695200-65695600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr11:65695200-65695600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:65695200-65695600	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr11:65695200-65695600	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr11:65695200-65695600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr11:65695200-65695600	Enhancers	Adipose Nuclei	Adipose

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