Variant report

Variant	rs3116616
Chromosome Location	chr13:51162913-51162914
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51148960..51151212-chr13:51161969..51163948,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1327646	0.80[EUR][1000 genomes]
rs1341637	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201762	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2225226	0.92[EUR][1000 genomes]
rs2408045	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3095527	0.80[EUR][1000 genomes]
rs3116599	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs3116600	0.85[EUR][1000 genomes]
rs3116601	0.85[EUR][1000 genomes]
rs3116602	0.91[EUR][1000 genomes]
rs3116603	0.91[EUR][1000 genomes]
rs3116604	0.90[EUR][1000 genomes]
rs3116605	0.90[EUR][1000 genomes]
rs3116606	0.90[EUR][1000 genomes]
rs3116607	0.82[EUR][1000 genomes]
rs3116613	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3116615	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3116617	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118903	0.81[EUR][1000 genomes]
rs3118905	1.00[JPT][hapmap]
rs3118906	1.00[JPT][hapmap]
rs3118909	0.85[EUR][1000 genomes]
rs3118910	0.85[EUR][1000 genomes]
rs3118912	0.91[EUR][1000 genomes]
rs3118913	0.90[EUR][1000 genomes]
rs3118914	0.90[EUR][1000 genomes]
rs3118915	0.93[EUR][1000 genomes]
rs3118918	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118919	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118920	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337757	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51150400-51167400	Weak transcription	HepG2	liver
2	chr13:51151200-51169600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr13:51156200-51167600	Weak transcription	Fetal Kidney	kidney
4	chr13:51158400-51164000	Enhancers	Fetal Muscle Leg	muscle
5	chr13:51159400-51168000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:51159400-51168000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:51159400-51170600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:51159600-51165000	Enhancers	Fetal Heart	heart
9	chr13:51159600-51168400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr13:51160000-51163600	Enhancers	Placenta	Placenta
11	chr13:51160000-51166600	Enhancers	Fetal Thymus	thymus
12	chr13:51160000-51168000	Weak transcription	Thymus	Thymus
13	chr13:51160200-51174000	Enhancers	Primary B cells from peripheral blood	blood
14	chr13:51160400-51163400	Weak transcription	Adipose Nuclei	Adipose
15	chr13:51160600-51164000	Enhancers	Primary B cells from cord blood	blood
16	chr13:51160800-51168000	Enhancers	Dnd41	blood
17	chr13:51161000-51163800	Enhancers	NHDF-Ad	bronchial
18	chr13:51161000-51164200	Enhancers	Primary hematopoietic stem cells	blood
19	chr13:51161200-51165000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:51161200-51165400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:51161200-51166000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr13:51161400-51164800	Enhancers	Osteobl	bone
23	chr13:51161400-51167600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:51161400-51168000	Weak transcription	Fetal Intestine Small	intestine
25	chr13:51161600-51163600	Enhancers	NH-A	brain
26	chr13:51161800-51163800	Enhancers	Right Atrium	heart
27	chr13:51161800-51164000	Enhancers	GM12878-XiMat	blood
28	chr13:51161800-51164600	Enhancers	HSMMtube	muscle
29	chr13:51162000-51163200	Enhancers	Fetal Muscle Trunk	muscle
30	chr13:51162000-51163600	Enhancers	Left Ventricle	heart
31	chr13:51162000-51163600	Enhancers	Right Ventricle	heart
32	chr13:51162000-51164800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr13:51162000-51165400	Enhancers	HSMM	muscle
34	chr13:51162000-51168000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr13:51162000-51168800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr13:51162200-51163400	Weak transcription	Lung	lung
37	chr13:51162200-51163600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:51162200-51163600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr13:51162200-51165200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:51162200-51165200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:51162200-51165200	Enhancers	NHEK	skin
42	chr13:51162200-51167400	Enhancers	HMEC	breast
43	chr13:51162200-51168000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr13:51162200-51172600	Weak transcription	Spleen	Spleen
45	chr13:51162400-51168800	Weak transcription	Fetal Lung	lung
46	chr13:51162400-51170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr13:51162600-51164400	Enhancers	NHLF	lung
48	chr13:51162600-51164600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:51162600-51164600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr13:51162600-51164800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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