Variant report

Variant	rs3212420
Chromosome Location	chr5:52322196-52322197
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	chr5:52284308..52287113-chr5:52321640..52324132,2	MCF-7	breast:
2	chr17:62236129..62238534-chr5:52321834..52323811,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10036871	0.90[AFR][1000 genomes]
rs10055193	0.93[AFR][1000 genomes]
rs10060638	0.90[AFR][1000 genomes]
rs10063405	0.85[AFR][1000 genomes]
rs10072303	1.00[AFR][1000 genomes]
rs28782593	0.89[AFR][1000 genomes]
rs3212405	0.90[AFR][1000 genomes]
rs3212406	0.90[AFR][1000 genomes]
rs3212407	0.90[AFR][1000 genomes]
rs3212409	0.90[AFR][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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52313800-52323400	Weak transcription	Spleen	Spleen
3	chr5:52314200-52328600	Weak transcription	Lung	lung
4	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:52314400-52323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:52314400-52323400	Weak transcription	Fetal Intestine Small	intestine
7	chr5:52314400-52326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:52317200-52327200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:52317400-52326800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:52317600-52326800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
12	chr5:52318400-52331800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:52318600-52322200	Enhancers	A549	lung
14	chr5:52318800-52327200	Genic enhancers	HMEC	breast
15	chr5:52319000-52325400	Enhancers	Brain Substantia Nigra	brain
16	chr5:52319200-52325400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:52319200-52326200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:52319200-52327600	Weak transcription	Fetal Intestine Large	intestine
19	chr5:52319600-52322200	Enhancers	HepG2	liver
20	chr5:52319600-52323200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:52319600-52323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:52319600-52326600	Weak transcription	Small Intestine	intestine
23	chr5:52320400-52322200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:52320600-52323000	Weak transcription	HUVEC	blood vessel
25	chr5:52320600-52323200	Weak transcription	NH-A	brain
26	chr5:52320600-52323400	Weak transcription	Osteobl	bone
27	chr5:52320600-52323600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:52320600-52326200	Weak transcription	Esophagus	oesophagus
29	chr5:52320600-52327400	Weak transcription	HSMM	muscle
30	chr5:52320600-52327600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:52320800-52323200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr5:52320800-52323200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:52320800-52323400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:52321000-52323200	Weak transcription	Brain Anterior Caudate	brain
35	chr5:52321000-52323400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:52321000-52323600	Weak transcription	NHDF-Ad	bronchial
37	chr5:52321000-52326600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr5:52321200-52322200	Enhancers	Brain Angular Gyrus	brain
39	chr5:52321400-52322800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:52321400-52323000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:52321400-52323400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:52321600-52323000	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:52321600-52323000	Weak transcription	Hela-S3	cervix
44	chr5:52321600-52323600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:52321600-52326800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr5:52321800-52323000	Enhancers	NHEK	skin
47	chr5:52321800-52323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:52321800-52323200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:52321800-52323200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:52321800-52326000	Weak transcription	Duodenum Mucosa	Duodenum

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