Variant report

Variant	rs7729717
Chromosome Location	chr5:178300998-178300999
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	chr5:178299499..178302283-chr5:178303072..178304596,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10039708	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11249599	0.82[EUR][1000 genomes]
rs11948175	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11948664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11948690	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949180	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949181	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949892	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11949941	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11950641	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11950746	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11952790	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11954382	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11955047	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11958804	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11958887	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11958941	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11960942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12186584	0.80[EUR][1000 genomes]
rs12187167	0.80[EUR][1000 genomes]
rs12553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1566106	0.90[EUR][1000 genomes]
rs35609799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35957383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56814168	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56872885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56932649	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56951084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57153194	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57426447	0.90[EUR][1000 genomes]
rs58354049	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58554591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58672680	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58679434	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58941917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59242428	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59736551	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59829327	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59849584	0.80[EUR][1000 genomes]
rs59994898	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60178472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60277514	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60417551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60601817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60813042	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61295075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61310482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61492890	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61744382	0.80[EUR][1000 genomes]
rs6600991	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6859174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6861717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6863160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6863202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6863603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865216	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6866591	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6870926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6877663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6878353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6882396	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6883566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6887256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6890083	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6894878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6895371	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7706558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7727497	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7729560	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7731067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:178289000-178301000	Strong transcription	Fetal Muscle Leg	muscle
6	chr5:178289000-178301600	Weak transcription	Stomach Mucosa	stomach
7	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
8	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:178290000-178302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:178290600-178301200	Strong transcription	Brain Cingulate Gyrus	brain
11	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
12	chr5:178292000-178303000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:178292200-178302200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:178292600-178301200	Strong transcription	Osteobl	bone
15	chr5:178292600-178305000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:178292600-178305200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr5:178292800-178301400	Strong transcription	Rectal Smooth Muscle	rectum
18	chr5:178293400-178301000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:178294200-178301400	Weak transcription	Hela-S3	cervix
20	chr5:178296000-178301200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:178296000-178305000	ZNF genes & repeats	A549	lung
22	chr5:178296000-178305200	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr5:178296000-178305400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
24	chr5:178296000-178319200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr5:178296200-178315600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr5:178296200-178319200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:178296400-178302400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:178296400-178311200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
29	chr5:178296400-178317600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr5:178297000-178301200	Strong transcription	Ovary	ovary
31	chr5:178297200-178315800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr5:178297400-178315600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
33	chr5:178297400-178317400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:178297400-178317400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
35	chr5:178297400-178317400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:178297600-178303600	ZNF genes & repeats	NHEK	skin
37	chr5:178297600-178305000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:178297600-178305200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr5:178297600-178317400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:178298000-178305200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
41	chr5:178298200-178302000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:178298200-178305000	Strong transcription	Psoas Muscle	Psoas
43	chr5:178298400-178301800	Strong transcription	HSMM	muscle
44	chr5:178298400-178305000	ZNF genes & repeats	Brain Substantia Nigra	brain
45	chr5:178298600-178301200	Weak transcription	Colonic Mucosa	Colon
46	chr5:178298600-178302000	Strong transcription	Placenta	Placenta
47	chr5:178298600-178302200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:178298600-178304000	Strong transcription	Fetal Kidney	kidney
49	chr5:178298600-178305000	ZNF genes & repeats	Brain Hippocampus Middle	brain
50	chr5:178298800-178301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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