Variant report

Variant	rs6430393
Chromosome Location	chr2:133855625-133855626
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	chr2:133850171..133852489-chr2:133854080..133856768,2	MCF-7	breast:
2	chr2:133427195..133430167-chr2:133854644..133856509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150551	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10194766	1.00[EUR][1000 genomes]
rs11889166	1.00[EUR][1000 genomes]
rs11894473	1.00[AMR][1000 genomes]
rs11895552	1.00[EUR][1000 genomes]
rs11900115	1.00[EUR][1000 genomes]
rs11901409	1.00[AMR][1000 genomes]
rs11903510	1.00[EUR][1000 genomes]
rs11903555	1.00[EUR][1000 genomes]
rs13388152	1.00[EUR][1000 genomes]
rs16822540	1.00[EUR][1000 genomes]
rs16822568	1.00[EUR][1000 genomes]
rs16822683	1.00[EUR][1000 genomes]
rs16822816	1.00[EUR][1000 genomes]
rs16823190	1.00[EUR][1000 genomes]
rs16847691	1.00[AMR][1000 genomes]
rs16855557	1.00[EUR][1000 genomes]
rs16857190	1.00[EUR][1000 genomes]
rs16857197	1.00[EUR][1000 genomes]
rs16857260	1.00[EUR][1000 genomes]
rs16857605	1.00[EUR][1000 genomes]
rs16858020	1.00[EUR][1000 genomes]
rs1836220	1.00[EUR][1000 genomes]
rs2069257	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2196167	1.00[AMR][1000 genomes]
rs2320320	1.00[EUR][1000 genomes]
rs35248736	0.82[AFR][1000 genomes]
rs35331541	0.91[AFR][1000 genomes]
rs56836351	1.00[EUR][1000 genomes]
rs56924347	1.00[AMR][1000 genomes]
rs57877229	0.97[AFR][1000 genomes]
rs58243416	1.00[AMR][1000 genomes]
rs58923924	1.00[AMR][1000 genomes]
rs59332303	0.95[AFR][1000 genomes]
rs59418354	0.97[AFR][1000 genomes]
rs59741799	1.00[EUR][1000 genomes]
rs61257975	1.00[EUR][1000 genomes]
rs6430379	1.00[EUR][1000 genomes]
rs6713080	1.00[EUR][1000 genomes]
rs6718899	1.00[EUR][1000 genomes]
rs6719117	1.00[AMR][1000 genomes]
rs6719786	1.00[EUR][1000 genomes]
rs6720246	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6722102	1.00[AMR][1000 genomes]
rs6725275	1.00[EUR][1000 genomes]
rs6727893	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs6732204	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6733114	1.00[EUR][1000 genomes]
rs6737234	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6738269	1.00[EUR][1000 genomes]
rs6761371	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72994884	1.00[EUR][1000 genomes]
rs7563261	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7568126	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7568144	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7568818	1.00[EUR][1000 genomes]
rs7576431	1.00[EUR][1000 genomes]
rs7578857	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7579940	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7584749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7585734	1.00[EUR][1000 genomes]
rs997377	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv916805	chr2:133664765-133924973	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv834381	chr2:133722671-133897994	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834382	chr2:133728399-133891418	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv875139	chr2:133777866-133929225	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv949546	chr2:133798832-133933491	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv470487	chr2:133811842-133875512	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv875140	chr2:133816484-133904829	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1008004	chr2:133827250-133954810	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv949629	chr2:133830379-134014961	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv1002197	chr2:133836002-133864689	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1001601	chr2:133838626-134005959	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv459452	chr2:133841008-133875512	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv583166	chr2:133841008-133875512	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133847000-133859200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:133853000-133867400	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:133854600-133865000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:133854800-133892000	Weak transcription	Left Ventricle	heart
5	chr2:133855200-133855800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:133855400-133856000	Active TSS	Ovary	ovary
7	chr2:133855400-133856200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:133855600-133855800	Enhancers	NHDF-Ad	bronchial
9	chr2:133855600-133856800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:133855600-133867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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