Variant report

Variant	rs3212417
Chromosome Location	chr5:52315112-52315113
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	chr5:52283546..52286213-chr5:52315102..52316776,2	MCF-7	breast:
2	chr5:52313064..52315275-chr5:52327348..52329688,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10042752	0.97[ASN][1000 genomes]
rs10058636	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10071255	1.00[ASN][1000 genomes]
rs10071580	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948978	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523395	0.88[CEU][hapmap]
rs1421941	0.97[ASN][1000 genomes]
rs16880636	1.00[ASN][1000 genomes]
rs1862639	0.84[CEU][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212402	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212412	1.00[ASN][1000 genomes]
rs55783963	1.00[ASN][1000 genomes]
rs67217308	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67835512	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883028	0.97[ASN][1000 genomes]
rs9292002	0.97[ASN][1000 genomes]
rs9292003	0.97[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	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52303400-52320400	Weak transcription	Fetal Brain Male	brain
2	chr5:52305200-52317200	Weak transcription	A549	lung
3	chr5:52307000-52333800	Weak transcription	Gastric	stomach
4	chr5:52311800-52317200	Weak transcription	NHLF	lung
5	chr5:52312000-52318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52312800-52315600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:52313200-52315800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:52313400-52315800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:52313400-52319400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:52313600-52318400	Weak transcription	NHDF-Ad	bronchial
11	chr5:52313600-52319800	Weak transcription	NH-A	brain
12	chr5:52313600-52321000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:52313800-52318800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:52313800-52319800	Weak transcription	Brain Angular Gyrus	brain
15	chr5:52313800-52320400	Weak transcription	Brain Anterior Caudate	brain
16	chr5:52313800-52323400	Weak transcription	Spleen	Spleen
17	chr5:52314000-52315600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:52314200-52315400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:52314200-52316400	Enhancers	HepG2	liver
20	chr5:52314200-52317400	Weak transcription	Brain Substantia Nigra	brain
21	chr5:52314200-52319600	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:52314200-52328600	Weak transcription	Lung	lung
23	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:52314400-52315400	Weak transcription	HMEC	breast
25	chr5:52314400-52316400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:52314400-52317200	Weak transcription	NHEK	skin
27	chr5:52314400-52323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:52314400-52323400	Weak transcription	Fetal Intestine Small	intestine
29	chr5:52314400-52326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:52314600-52315200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:52314600-52316200	Enhancers	HUVEC	blood vessel
32	chr5:52314800-52317200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:52315000-52315400	Weak transcription	Hela-S3	cervix

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