Variant report

Variant	rs56093222
Chromosome Location	chr5:179189865-179189866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179189824..179191528-chr5:179247114..179249290,2	MCF-7	breast:
2	chr5:179188650..179190562-chr5:179226807..179228965,2	MCF-7	breast:
3	chr5:179189848..179190448-chr5:179297466..179298126,2	K562	blood:
4	chr5:179158835..179161436-chr5:179188218..179192276,6	MCF-7	breast:
5	chr5:179183405..179185211-chr5:179188003..179190913,2	MCF-7	breast:
6	chr5:179189775..179190581-chr5:179231187..179232028,2	K562	blood:
7	chr5:179189767..179190816-chr5:179222590..179224521,15	MCF-7	breast:
8	chr5:179185016..179191633-chr5:179218101..179224928,12	MCF-7	breast:
9	chr5:179187933..179190837-chr5:179234085..179236035,2	MCF-7	breast:
10	chr5:179124402..179127168-chr5:179188408..179191090,3	MCF-7	breast:
11	chr5:179186999..179190414-chr5:179192166..179194492,3	MCF-7	breast:
12	chr5:179188510..179190783-chr5:179246852..179250519,7	K562	blood:
13	chr5:179158546..179161718-chr5:179184592..179191275,7	MCF-7	breast:
14	chr5:179189040..179191704-chr5:179221605..179224546,3	MCF-7	breast:
15	chr5:179189180..179191928-chr5:179192012..179195048,3	K562	blood:
16	chr5:179188774..179192649-chr5:179245020..179250577,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000161021	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs2291417	0.91[AMR][1000 genomes]
rs2291418	0.91[AMR][1000 genomes]
rs55800082	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55815501	1.00[EUR][1000 genomes]
rs55915939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55952102	0.94[EUR][1000 genomes]
rs55967209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56719864	0.91[AFR][1000 genomes]
rs57463529	0.96[AFR][1000 genomes]
rs58722253	0.96[AFR][1000 genomes]
rs58826518	0.91[AMR][1000 genomes]
rs59108011	0.84[AFR][1000 genomes]
rs59566858	0.96[AFR][1000 genomes]
rs59651103	0.96[AFR][1000 genomes]
rs59721505	0.96[AFR][1000 genomes]
rs59745533	0.96[AFR][1000 genomes]
rs59824837	0.96[AFR][1000 genomes]
rs60485189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60716268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60910702	0.87[AFR][1000 genomes]
rs61682673	0.96[AFR][1000 genomes]
rs66465242	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66685266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66686562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66995745	0.91[AMR][1000 genomes]
rs67211456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67637906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67832593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67879510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67952129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865507	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807319	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807328	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807332	1.00[EUR][1000 genomes]
rs72807337	1.00[EUR][1000 genomes]
rs72809763	0.94[EUR][1000 genomes]
rs72809769	0.94[EUR][1000 genomes]
rs72809771	0.94[EUR][1000 genomes]
rs72809773	0.94[EUR][1000 genomes]
rs72809775	1.00[EUR][1000 genomes]
rs72809781	1.00[EUR][1000 genomes]
rs72809782	1.00[EUR][1000 genomes]
rs72809783	1.00[EUR][1000 genomes]
rs72809785	1.00[EUR][1000 genomes]
rs72809787	1.00[EUR][1000 genomes]
rs72809790	1.00[EUR][1000 genomes]
rs72809792	1.00[EUR][1000 genomes]
rs72809794	1.00[EUR][1000 genomes]
rs72809795	1.00[EUR][1000 genomes]
rs72809796	1.00[EUR][1000 genomes]
rs72809798	1.00[EUR][1000 genomes]
rs72809802	1.00[EUR][1000 genomes]
rs73338115	0.88[AFR][1000 genomes]
rs73342167	0.96[AFR][1000 genomes]
rs73347986	0.96[AFR][1000 genomes]
rs73349908	0.96[AFR][1000 genomes]
rs73351620	0.84[AFR][1000 genomes]
rs73351626	0.84[AFR][1000 genomes]
rs73351628	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179162000-179190400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:179174400-179192200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:179182600-179192400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:179183200-179192600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:179185800-179190000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:179185800-179190800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr5:179186000-179191200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr5:179186000-179192600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr5:179186400-179191000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:179186400-179191200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:179186600-179192400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:179186800-179191000	Enhancers	Fetal Thymus	thymus
13	chr5:179186800-179191400	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr5:179187600-179190800	Enhancers	GM12878-XiMat	blood
15	chr5:179187600-179192200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr5:179188000-179191400	Enhancers	Duodenum Mucosa	Duodenum
17	chr5:179188000-179192600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:179188200-179191000	Enhancers	Primary B cells from cord blood	blood
19	chr5:179188400-179191000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:179188400-179191200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:179188400-179191200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:179188400-179191400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr5:179188400-179192400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:179188600-179190200	Enhancers	Primary T cells from cord blood	blood
25	chr5:179188600-179190200	Enhancers	Primary hematopoietic stem cells	blood
26	chr5:179188600-179190200	Enhancers	Stomach Smooth Muscle	stomach
27	chr5:179188600-179191000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:179188600-179191000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:179188600-179191000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr5:179188600-179191000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:179188600-179191000	Enhancers	Small Intestine	intestine
32	chr5:179188600-179191000	Enhancers	Stomach Mucosa	stomach
33	chr5:179188600-179191200	Enhancers	Primary B cells from peripheral blood	blood
34	chr5:179188600-179191200	Enhancers	Brain Hippocampus Middle	brain
35	chr5:179188600-179191200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr5:179188600-179191400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:179188600-179191600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr5:179188600-179192400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:179188600-179192400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr5:179188600-179192600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:179188600-179192600	Enhancers	Liver	Liver
42	chr5:179188600-179193000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:179188600-179193000	Enhancers	HMEC	breast
44	chr5:179188600-179193600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:179188800-179190000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:179188800-179190000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:179188800-179190000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:179188800-179190000	Enhancers	Psoas Muscle	Psoas
49	chr5:179188800-179190400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:179188800-179190600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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