Variant report

Variant	rs1380609
Chromosome Location	chr3:53714176-53714177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53708590..53712002-chr3:53712853..53715298,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11915963	1.00[YRI][hapmap]
rs11926741	1.00[YRI][hapmap]
rs13065154	1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs1380606	0.88[MKK][hapmap]
rs1460116	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1599231	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2250736	0.86[MKK][hapmap]
rs2612018	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3774480	1.00[YRI][hapmap]
rs3774527	1.00[YRI][hapmap]
rs3821856	1.00[YRI][hapmap]
rs3821858	1.00[YRI][hapmap]
rs898408	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs898415	0.88[MKK][hapmap]
rs898416	0.81[MKK][hapmap]
rs898422	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53713200-53716000	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53713600-53714400	Enhancers	Fetal Stomach	stomach
4	chr3:53713600-53714600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:53713600-53714600	Enhancers	Fetal Brain Female	brain
6	chr3:53713600-53714600	Enhancers	Fetal Lung	lung
7	chr3:53713600-53715000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:53713800-53714200	Flanking Active TSS	Fetal Brain Male	brain
9	chr3:53713800-53714600	Enhancers	Colon Smooth Muscle	Colon
10	chr3:53713800-53714600	Enhancers	Fetal Muscle Leg	muscle
11	chr3:53713800-53714600	Enhancers	Psoas Muscle	Psoas
12	chr3:53713800-53715800	Strong transcription	Fetal Intestine Small	intestine
13	chr3:53713800-53717600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:53714000-53714200	Enhancers	Fetal Heart	heart
15	chr3:53714000-53714200	Enhancers	Fetal Kidney	kidney
16	chr3:53714000-53714200	Enhancers	Lung	lung
17	chr3:53714000-53714400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:53714000-53714400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:53714000-53714400	Active TSS	Stomach Smooth Muscle	stomach
20	chr3:53714000-53714600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:53714000-53714600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
22	chr3:53714000-53714600	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:53714000-53714600	Enhancers	Brain Substantia Nigra	brain
24	chr3:53714000-53714600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr3:53714000-53714600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr3:53714000-53714600	Enhancers	Left Ventricle	heart
27	chr3:53714000-53714600	Enhancers	Right Atrium	heart
28	chr3:53714000-53714600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:53714000-53715400	Enhancers	Brain Angular Gyrus	brain

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