Variant report

Variant	rs7727497
Chromosome Location	chr5:178288761-178288762
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178154802..178159439-chr5:178284936..178288781,7	MCF-7	breast:
2	chr5:178286798..178288918-chr5:178487242..178488938,2	MCF-7	breast:
3	chr5:178285646..178289279-chr5:178321547..178324884,4	MCF-7	breast:
4	chr5:177640785..177642286-chr5:178288319..178291268,2	K562	blood:
5	chr5:178156014..178158845-chr5:178285994..178289826,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198939	Chromatin interaction
ENSG00000177932	Chromatin interaction
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10039708	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11948175	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11948664	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11948690	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11949180	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11949181	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11949892	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11949941	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11950641	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11950746	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11952790	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11954382	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11955047	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11958804	0.80[AMR][1000 genomes]
rs11958887	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11958941	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11960942	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12553	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35609799	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35957383	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56814168	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56872885	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56932649	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56951084	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57153194	0.82[EUR][1000 genomes]
rs58354049	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58554591	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58672680	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58679434	0.90[EUR][1000 genomes]
rs58941917	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59242428	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59736551	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs59829327	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59994898	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60178472	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60277514	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60417551	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60601817	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60813042	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61295075	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61310482	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61492890	0.83[EUR][1000 genomes]
rs6600991	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6859174	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6861717	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6863160	0.83[EUR][1000 genomes]
rs6863202	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6863603	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6865216	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6866591	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6870926	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6877663	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6878353	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6882396	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6883566	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6887256	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6890083	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6894878	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6895371	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7706558	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7729560	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7729717	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7731067	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv823352	chr5:178279625-178296623	Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178286600-178288800	Active TSS	Muscle Satellite Cultured Cells	--
2	chr5:178287600-178289600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:178287600-178289600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr5:178287600-178289600	Weak transcription	Right Atrium	heart
5	chr5:178287600-178289800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:178287600-178289800	Weak transcription	Fetal Thymus	thymus
7	chr5:178287600-178291000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:178287600-178292000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:178287600-178292200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:178287600-178292400	Weak transcription	Aorta	Aorta
11	chr5:178287600-178292600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:178287600-178294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:178287600-178296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:178287800-178288800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:178287800-178288800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:178287800-178288800	Weak transcription	NH-A	brain
18	chr5:178287800-178289200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:178287800-178289600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:178287800-178289600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:178287800-178289800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:178287800-178293200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:178288000-178288800	Enhancers	Rectal Smooth Muscle	rectum
24	chr5:178288000-178289600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr5:178288200-178288800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:178288200-178288800	Enhancers	Primary B cells from peripheral blood	blood
27	chr5:178288200-178288800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:178288200-178288800	Genic enhancers	Fetal Lung	lung
29	chr5:178288200-178288800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr5:178288200-178288800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr5:178288200-178288800	Flanking Active TSS	NHEK	skin
32	chr5:178288200-178289000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr5:178288200-178289000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr5:178288200-178289000	Enhancers	Fetal Brain Male	brain
35	chr5:178288200-178289000	Genic enhancers	Fetal Muscle Leg	muscle
36	chr5:178288200-178289200	Enhancers	Left Ventricle	heart
37	chr5:178288200-178290200	Genic enhancers	K562	blood
38	chr5:178288200-178295000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr5:178288400-178288800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
41	chr5:178288400-178288800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr5:178288400-178288800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:178288400-178288800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:178288400-178288800	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr5:178288400-178288800	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr5:178288400-178288800	Flanking Active TSS	HMEC	breast
47	chr5:178288400-178288800	Flanking Active TSS	NHDF-Ad	bronchial
48	chr5:178288400-178289000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr5:178288400-178289000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr5:178288400-178289000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain

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