Variant report

Variant	rs4976798
Chromosome Location	chr5:178021280-178021281
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	chr5:178019997..178022007-chr5:178050984..178053956,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10035557	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051137	0.97[ASN][1000 genomes]
rs10061455	0.87[ASN][1000 genomes]
rs10061883	0.87[ASN][1000 genomes]
rs10064009	0.87[ASN][1000 genomes]
rs10065419	0.81[ASN][1000 genomes]
rs10070794	0.87[ASN][1000 genomes]
rs10073925	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479501	0.87[ASN][1000 genomes]
rs11742564	0.91[ASN][1000 genomes]
rs11744815	0.91[ASN][1000 genomes]
rs11748909	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654185	0.87[ASN][1000 genomes]
rs12654187	0.87[ASN][1000 genomes]
rs12719855	0.81[ASN][1000 genomes]
rs13161074	0.83[ASN][1000 genomes]
rs13360296	0.94[ASN][1000 genomes]
rs1472457	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1967419	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2335442	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262021	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262028	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262036	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388749	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073633	0.87[ASN][1000 genomes]
rs4077796	0.95[ASN][1000 genomes]
rs4079109	0.87[ASN][1000 genomes]
rs4079111	0.87[ASN][1000 genomes]
rs4079112	0.87[ASN][1000 genomes]
rs4301240	0.87[ASN][1000 genomes]
rs4413550	0.87[ASN][1000 genomes]
rs4418123	0.87[ASN][1000 genomes]
rs4437394	0.87[ASN][1000 genomes]
rs4521498	0.91[ASN][1000 genomes]
rs6600942	0.89[ASN][1000 genomes]
rs6866336	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866952	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6869889	0.89[ASN][1000 genomes]
rs6871074	0.92[ASN][1000 genomes]
rs6874126	0.81[ASN][1000 genomes]
rs6877022	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs721142	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73353860	0.85[ASN][1000 genomes]
rs73353883	0.87[ASN][1000 genomes]
rs752043	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707891	0.91[ASN][1000 genomes]
rs7715291	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720708	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736565	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776153	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883216	chr5:178002325-178025087	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178017800-178023200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:178017800-178031400	Weak transcription	Pancreas	Pancrea
3	chr5:178017800-178033400	Weak transcription	Esophagus	oesophagus
4	chr5:178017800-178033400	Weak transcription	Gastric	stomach
5	chr5:178017800-178033400	Weak transcription	Right Atrium	heart
6	chr5:178018000-178026400	Weak transcription	Placenta	Placenta
7	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:178018200-178021400	Weak transcription	Brain Substantia Nigra	brain
9	chr5:178018200-178021400	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:178018200-178021800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:178018200-178022000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:178018200-178022200	Weak transcription	Liver	Liver
13	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
15	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
16	chr5:178018400-178023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:178018400-178024200	Weak transcription	Osteobl	bone
18	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:178018600-178021400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:178018600-178021800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:178018600-178022000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:178018600-178026400	Weak transcription	HSMMtube	muscle
23	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:178018800-178022200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:178018800-178024600	Weak transcription	Left Ventricle	heart
26	chr5:178019000-178022200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:178019000-178022400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:178019000-178029600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:178019000-178031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:178019200-178021800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:178019200-178024200	Weak transcription	Fetal Thymus	thymus
32	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
33	chr5:178019600-178027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:178020600-178028000	Weak transcription	NHLF	lung
35	chr5:178020800-178021600	Strong transcription	Fetal Stomach	stomach
36	chr5:178021000-178021400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
37	chr5:178021000-178021400	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr5:178021000-178021400	ZNF genes & repeats	Lung	lung
39	chr5:178021000-178021400	ZNF genes & repeats	Spleen	Spleen
40	chr5:178021200-178021400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:178021200-178021400	ZNF genes & repeats	Fetal Intestine Small	intestine
42	chr5:178021200-178021400	Enhancers	Small Intestine	intestine
43	chr5:178021200-178021600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:178021200-178021600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
45	chr5:178021200-178021600	ZNF genes & repeats	Ovary	ovary
46	chr5:178021200-178021600	ZNF genes & repeats	HSMM	muscle
47	chr5:178021200-178021800	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr5:178021200-178023200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
49	chr5:178021200-178023600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
50	chr5:178021200-178024000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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