Variant report

Variant	rs1197296
Chromosome Location	chr3:133108978-133108979
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	chr3:133103166..133105237-chr3:133107966..133110867,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1109858	0.82[JPT][hapmap]
rs1114630	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs1197287	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1197288	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1197293	0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1197297	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1197298	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1197299	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1197301	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1197302	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1197304	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1197305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197306	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1197308	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1197309	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1197313	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1197314	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1201671	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1201673	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12631678	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1619552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1619622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1708376	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1708377	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708384	0.97[ASN][1000 genomes]
rs1708385	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1795101	0.82[JPT][hapmap]
rs1795104	0.91[ASN][1000 genomes]
rs1795107	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2089987	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2670179	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2699880	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2699882	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732572	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4854583	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4854719	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4854720	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56181416	0.88[ASN][1000 genomes]
rs656721	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs6780144	0.90[ASN][1000 genomes]
rs6802663	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs938231	0.85[ASN][1000 genomes]
rs9850193	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9853752	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9853757	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv460857	chr3:133101390-133122216	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv591801	chr3:133101390-133122216	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1197296	RAB6B	cis	parietal	SCAN
rs1197296	MSL2	cis	parietal	SCAN
rs1197296	STAG1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133094000-133109000	Weak transcription	HSMM	muscle
2	chr3:133094800-133110400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:133099000-133117000	Weak transcription	Placenta	Placenta
4	chr3:133099600-133122600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:133100800-133111600	Weak transcription	HSMMtube	muscle
6	chr3:133102400-133112400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:133103400-133109000	Weak transcription	Fetal Stomach	stomach
8	chr3:133103400-133111600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:133103400-133112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:133103400-133115200	Weak transcription	Lung	lung
11	chr3:133103400-133123200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:133103400-133123600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:133103800-133109000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:133103800-133109200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:133103800-133109200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:133103800-133109400	Weak transcription	Fetal Brain Male	brain
17	chr3:133103800-133109600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:133103800-133109800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:133103800-133112000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:133103800-133115800	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:133103800-133118600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:133103800-133123800	Weak transcription	Brain Anterior Caudate	brain
23	chr3:133104000-133112000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:133104000-133122200	Weak transcription	Brain Substantia Nigra	brain
25	chr3:133104200-133109000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:133104400-133112000	Strong transcription	Fetal Brain Female	brain
27	chr3:133104400-133131400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:133107200-133123800	Weak transcription	Fetal Thymus	thymus
29	chr3:133108000-133109000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:133108000-133115200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:133108200-133110200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:133108200-133112800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:133108600-133109000	Genic enhancers	Fetal Lung	lung
34	chr3:133108800-133112800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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