Variant report

Variant	rs11720353
Chromosome Location	chr3:120428621-120428622
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	chr3:120417863..120420778-chr3:120426396..120428792,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11708525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708642	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11712360	0.83[ASN][1000 genomes]
rs11713594	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714216	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716584	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11718363	0.84[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs11719207	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11719896	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11720614	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs167722	0.82[CEU][hapmap]
rs17183618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17184204	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17243218	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs17243933	0.83[ASN][1000 genomes]
rs2059331	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2229308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2292170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2877413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34319994	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34565470	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41365345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55663109	0.80[ASN][1000 genomes]
rs55697401	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55869122	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56140323	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56267829	0.93[ASN][1000 genomes]
rs6438590	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183728	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73183730	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7637037	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7647895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11720353	MYSM1	trans	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120398200-120430200	Weak transcription	NHEK	skin
2	chr3:120398200-120438000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:120398800-120442200	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:120402800-120456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:120405600-120436800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:120406400-120436600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:120408400-120429400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:120411000-120436600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:120412800-120435600	Weak transcription	NH-A	brain
10	chr3:120412800-120438000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:120415000-120438000	Weak transcription	HepG2	liver
12	chr3:120416400-120436800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:120416400-120437200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:120416400-120437800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:120416400-120460600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:120416600-120438000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:120416800-120460600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:120417600-120456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:120418800-120429400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:120419000-120450800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:120420200-120428800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:120422000-120438000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:120422000-120438000	Weak transcription	Fetal Stomach	stomach
24	chr3:120422000-120438000	Weak transcription	Fetal Thymus	thymus
25	chr3:120422000-120438000	Weak transcription	Left Ventricle	heart
26	chr3:120422200-120437000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:120422200-120438000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:120422200-120438000	Weak transcription	Fetal Kidney	kidney
29	chr3:120422200-120441000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:120422200-120446800	Weak transcription	Ovary	ovary
31	chr3:120422400-120437000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:120422400-120438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:120422400-120444200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:120422600-120437800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:120423000-120433200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:120423000-120460200	Weak transcription	HUVEC	blood vessel
37	chr3:120423200-120437200	Weak transcription	GM12878-XiMat	blood
38	chr3:120423400-120429400	Weak transcription	Primary T cells from cord blood	blood
39	chr3:120423400-120437400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:120423400-120438000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:120423400-120441000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:120423600-120438000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:120423600-120447200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:120423800-120437200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:120424200-120437000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:120424400-120436600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:120424400-120438000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:120424400-120446800	Weak transcription	Fetal Intestine Large	intestine
49	chr3:120424600-120450200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:120424800-120430200	Weak transcription	NHDF-Ad	bronchial

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