Variant report

Variant	rs28654446
Chromosome Location	chr5:178958747-178958748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178958463..178961720-chr5:178975691..178978032,4	MCF-7	breast:
2	chr5:178958501..178962397-chr5:178966368..178969379,3	K562	blood:

Variant related genes	Relation type
ENSG00000176783	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13185221	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28495954	0.95[ASN][1000 genomes]
rs28583161	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28810156	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28865714	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4701191	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58858932	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59757520	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6887492	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7380633	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv34709	chr5:178720968-178961710	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv2757148	chr5:178720968-178961872	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv34254	chr5:178749394-178961710	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv883260	chr5:178828854-178961710	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
10	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
11	nsv5158	chr5:178946891-178968477	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1022509	chr5:178950829-179002751	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv883269	chr5:178951106-179031595	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
15	nsv1015477	chr5:178954409-179016804	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv883271	chr5:178955046-179031595	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178956400-178958800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:178956600-178958800	Flanking Active TSS	Dnd41	blood
3	chr5:178957600-178962400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:178957800-178958800	Enhancers	Primary hematopoietic stem cells	blood
5	chr5:178957800-178960000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:178957800-178961400	Weak transcription	K562	blood
7	chr5:178958000-178958800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr5:178958000-178961000	Weak transcription	Right Atrium	heart
9	chr5:178958000-178961200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:178958000-178961400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:178958000-178961400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:178958000-178961400	Weak transcription	Liver	Liver
13	chr5:178958000-178961400	Weak transcription	Thymus	Thymus
14	chr5:178958000-178961600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:178958000-178961800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:178958000-178961800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:178958000-178962200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:178958000-178962200	Weak transcription	Spleen	Spleen
19	chr5:178958000-178962400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:178958000-178976800	Weak transcription	Fetal Intestine Small	intestine
21	chr5:178958000-178977000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:178958200-178959000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:178958200-178961200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:178958200-178961400	Weak transcription	HepG2	liver
25	chr5:178958200-178961600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:178958200-178961600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:178958200-178963200	Weak transcription	Osteobl	bone
28	chr5:178958400-178958800	Active TSS	Colon Smooth Muscle	Colon
29	chr5:178958400-178960400	Weak transcription	Primary B cells from cord blood	blood
30	chr5:178958400-178961400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:178958600-178958800	Enhancers	Primary B cells from peripheral blood	blood
32	chr5:178958600-178958800	Enhancers	GM12878-XiMat	blood

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