Variant report

Variant	rs62283538
Chromosome Location	chr3:99678943-99678944
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	chr3:99665125..99667947-chr3:99677482..99680159,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13063594	0.82[EUR][1000 genomes]
rs13076199	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13084413	0.85[AFR][1000 genomes]
rs13089461	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13095282	0.82[EUR][1000 genomes]
rs13096116	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097830	0.82[EUR][1000 genomes]
rs13100490	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34174004	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35098023	0.82[EUR][1000 genomes]
rs36077012	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791889	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626245	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7649862	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99669200-99679800	Weak transcription	Fetal Intestine Small	intestine
3	chr3:99670800-99679200	Weak transcription	Small Intestine	intestine
4	chr3:99671400-99679400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:99671600-99684200	Weak transcription	NHEK	skin
6	chr3:99671600-99688200	Weak transcription	Primary T cells from cord blood	blood
7	chr3:99672600-99680000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:99672800-99680000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:99673000-99679400	Weak transcription	Osteobl	bone
10	chr3:99673000-99680800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:99673000-99681000	Weak transcription	HSMM	muscle
12	chr3:99676200-99679200	Weak transcription	Stomach Mucosa	stomach
13	chr3:99676200-99679400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:99676400-99679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:99676800-99679000	Weak transcription	HepG2	liver
16	chr3:99677200-99679400	Enhancers	Psoas Muscle	Psoas
17	chr3:99677400-99679200	Weak transcription	Fetal Kidney	kidney
18	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:99677600-99679000	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:99677600-99679000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:99677600-99679200	Weak transcription	Adipose Nuclei	Adipose
22	chr3:99677600-99679200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:99677600-99679400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:99677600-99680200	Weak transcription	Fetal Heart	heart
25	chr3:99677600-99680400	Weak transcription	Left Ventricle	heart
26	chr3:99677600-99680800	Weak transcription	Right Ventricle	heart
27	chr3:99677600-99684400	Weak transcription	Fetal Stomach	stomach
28	chr3:99677600-99684400	Weak transcription	Pancreas	Pancrea
29	chr3:99677600-99684600	Weak transcription	Lung	lung
30	chr3:99677600-99692600	Weak transcription	Fetal Lung	lung
31	chr3:99677800-99679200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:99677800-99679200	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:99677800-99679200	Weak transcription	NHDF-Ad	bronchial
34	chr3:99677800-99680600	Weak transcription	HSMMtube	muscle
35	chr3:99677800-99680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:99677800-99680800	Weak transcription	Right Atrium	heart
37	chr3:99678200-99680800	Weak transcription	Ovary	ovary
38	chr3:99678800-99679400	Enhancers	Aorta	Aorta
39	chr3:99678800-99682400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:99678800-99691800	Enhancers	Skeletal Muscle Female	skeletal muscle

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