Variant report

Variant	rs7617345
Chromosome Location	chr3:50419348-50419349
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	chr3:50403729..50405673-chr3:50419151..50420846,2	MCF-7	breast:
2	chr3:50419009..50422090-chr3:50424618..50428241,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271858	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1034408	0.81[AFR][1000 genomes]
rs11914549	0.93[AFR][1000 genomes]
rs28593422	0.83[AFR][1000 genomes]
rs41305886	0.89[AFR][1000 genomes]
rs4422301	0.90[AFR][1000 genomes]
rs55876418	0.92[AFR][1000 genomes]
rs56114301	0.81[AFR][1000 genomes]
rs56249615	0.81[AFR][1000 genomes]
rs56258146	0.81[AFR][1000 genomes]
rs56287038	0.96[AFR][1000 genomes]
rs57405128	0.92[AFR][1000 genomes]
rs57415469	0.81[AFR][1000 genomes]
rs58415636	0.94[AFR][1000 genomes]
rs59012751	0.81[AFR][1000 genomes]
rs59790001	0.90[AFR][1000 genomes]
rs60149721	0.81[AFR][1000 genomes]
rs60273100	0.81[AFR][1000 genomes]
rs6446203	0.90[AFR][1000 genomes]
rs6770258	0.92[AFR][1000 genomes]
rs6770669	0.92[AFR][1000 genomes]
rs73832879	0.82[AFR][1000 genomes]
rs73832881	0.83[AFR][1000 genomes]
rs73833366	0.82[AFR][1000 genomes]
rs73833371	0.81[AFR][1000 genomes]
rs73833372	0.81[AFR][1000 genomes]
rs73833373	0.90[AFR][1000 genomes]
rs73833386	0.81[AFR][1000 genomes]
rs743755	0.82[AFR][1000 genomes]
rs7610830	0.90[AFR][1000 genomes]
rs7612820	0.81[AFR][1000 genomes]
rs7625295	0.81[AFR][1000 genomes]
rs7634307	0.81[AFR][1000 genomes]
rs7640842	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
8	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
9	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
12	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
14	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
15	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
16	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
17	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
18	nsv876778	chr3:50413707-50465518	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50408800-50423800	Weak transcription	Fetal Brain Female	brain
2	chr3:50409000-50419600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:50409200-50420200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:50411400-50422600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:50411400-50430000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:50412800-50428000	Weak transcription	Right Ventricle	heart
7	chr3:50413200-50421000	Weak transcription	Lung	lung
8	chr3:50414000-50420600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:50415000-50419600	Weak transcription	Ovary	ovary
10	chr3:50415200-50428400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:50416000-50421200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:50416800-50419600	Weak transcription	Fetal Stomach	stomach
13	chr3:50416800-50420200	Weak transcription	Spleen	Spleen
14	chr3:50416800-50420600	Enhancers	Brain Germinal Matrix	brain
15	chr3:50417000-50428000	Weak transcription	Gastric	stomach
16	chr3:50417400-50420400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:50417600-50421400	Enhancers	Fetal Muscle Leg	muscle
18	chr3:50418200-50420000	Enhancers	Fetal Thymus	thymus
19	chr3:50418200-50421600	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:50418600-50419400	Enhancers	Stomach Mucosa	stomach
21	chr3:50418800-50420600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:50419000-50419800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:50419200-50419600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:50419200-50419600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:50419200-50419600	Enhancers	Fetal Brain Male	brain
26	chr3:50419200-50419800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:50419200-50420400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:50419200-50421400	Enhancers	Fetal Kidney	kidney

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