Variant report

Variant	rs378720
Chromosome Location	chr22:29760139-29760140
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	chr22:29700727..29703108-chr22:29758204..29760542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185340	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1807503	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2002566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267135	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267136	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283852	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283853	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283854	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301586	0.81[ASN][1000 genomes]
rs2348468	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2881921	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34234634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788412	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3963293	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820809	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4823032	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5752905	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752906	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752907	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763144	0.90[ASN][1000 genomes]
rs5763171	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763172	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763173	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763179	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763182	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763184	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763189	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763190	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006103	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006104	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6006109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6006112	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006113	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006115	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737883	0.89[ASN][1000 genomes]
rs9613859	0.81[ASN][1000 genomes]
rs9613878	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv966099	chr22:29755726-29762172	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	nsv914961	chr22:29755888-29817506	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv914962	chr22:29755888-29823768	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	esv2580719	chr22:29759273-29816494	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29723000-29765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr22:29739000-29762800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr22:29741000-29782800	Weak transcription	Hela-S3	cervix
4	chr22:29741800-29760200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr22:29745000-29765200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:29745600-29763400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr22:29750600-29765200	Weak transcription	NHDF-Ad	bronchial
8	chr22:29750600-29766800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr22:29750800-29764400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:29753000-29777600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr22:29754600-29770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr22:29754800-29765200	Weak transcription	HSMM	muscle
13	chr22:29755000-29765200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:29755000-29772200	Weak transcription	Aorta	Aorta
15	chr22:29755000-29783800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:29755200-29765000	Weak transcription	NH-A	brain
17	chr22:29755200-29773800	Weak transcription	Stomach Mucosa	stomach
18	chr22:29755200-29781000	Weak transcription	Fetal Brain Male	brain
19	chr22:29755200-29782800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr22:29755400-29762000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr22:29755400-29764600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr22:29755400-29765400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:29755400-29783600	Weak transcription	Fetal Kidney	kidney
24	chr22:29755600-29762000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr22:29755600-29763800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr22:29755600-29763800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr22:29755600-29771400	Weak transcription	Psoas Muscle	Psoas
28	chr22:29755600-29778600	Weak transcription	Fetal Lung	lung
29	chr22:29755800-29776600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr22:29756000-29760800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr22:29756000-29762000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr22:29756000-29762000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:29756000-29762000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr22:29756000-29762000	Weak transcription	Brain Hippocampus Middle	brain
35	chr22:29756000-29762000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr22:29756000-29762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr22:29756000-29763000	Strong transcription	Fetal Intestine Small	intestine
38	chr22:29756000-29764000	Weak transcription	Brain Substantia Nigra	brain
39	chr22:29756000-29764200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr22:29756000-29764400	Weak transcription	Brain Angular Gyrus	brain
41	chr22:29756000-29764400	Weak transcription	NHEK	skin
42	chr22:29756000-29764600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr22:29756000-29764600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr22:29756000-29764600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr22:29756000-29765200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr22:29756000-29765200	Weak transcription	HepG2	liver
47	chr22:29756000-29765200	Weak transcription	Osteobl	bone
48	chr22:29756000-29765400	Weak transcription	A549	lung
49	chr22:29756000-29766400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr22:29756000-29766400	Weak transcription	Stomach Smooth Muscle	stomach

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