Variant report

Variant	rs73979046
Chromosome Location	chr17:16924405-16924406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16920777..16926602-chr17:16943525..16948995,8	MCF-7	breast:
2	chr17:16923260..16925095-chr17:16929732..16931336,2	MCF-7	breast:
3	chr17:16922760..16925384-chr17:16927836..16930121,3	K562	blood:
4	chr17:16921667..16924582-chr17:17139472..17141116,2	MCF-7	breast:
5	chr17:16924258..16925128-chr21:37692186..37693016,2	Hela-S3	cervix:
6	chr17:16922760..16926151-chr17:16927403..16930298,5	K562	blood:

Variant related genes	Relation type
ENSG00000154803	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000159256	Chromatin interaction
ENSG00000133030	Chromatin interaction
ENSG00000273199	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10048152	1.00[EUR][1000 genomes]
rs1131632	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16961406	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28829096	1.00[EUR][1000 genomes]
rs4485421	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55792503	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56247606	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56343767	1.00[EUR][1000 genomes]
rs56912118	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58169814	1.00[EUR][1000 genomes]
rs58377774	0.84[AFR][1000 genomes]
rs58442149	1.00[EUR][1000 genomes]
rs58690840	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58702370	1.00[EUR][1000 genomes]
rs60029796	1.00[EUR][1000 genomes]
rs60192272	1.00[EUR][1000 genomes]
rs60332371	1.00[EUR][1000 genomes]
rs60364428	1.00[EUR][1000 genomes]
rs60545734	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60697210	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60890438	1.00[EUR][1000 genomes]
rs61024568	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61218165	1.00[EUR][1000 genomes]
rs61608940	1.00[EUR][1000 genomes]
rs7219836	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7223145	1.00[EUR][1000 genomes]
rs7223758	1.00[EUR][1000 genomes]
rs73979025	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979028	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979045	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979047	0.83[AFR][1000 genomes]
rs73979048	1.00[EUR][1000 genomes]
rs73979049	1.00[EUR][1000 genomes]
rs73979056	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979057	1.00[EUR][1000 genomes]
rs73979063	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979079	1.00[EUR][1000 genomes]
rs73979080	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979088	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979096	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979097	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981903	1.00[EUR][1000 genomes]
rs73981904	1.00[EUR][1000 genomes]
rs8079021	1.00[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	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16917400-16926200	Enhancers	Stomach Mucosa	stomach
2	chr17:16918000-16926200	Enhancers	Placenta	Placenta
3	chr17:16918800-16930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:16919800-16926200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:16920200-16926200	Enhancers	Pancreas	Pancrea
6	chr17:16921000-16926200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr17:16921200-16925400	Enhancers	HMEC	breast
8	chr17:16921400-16924800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:16922400-16925400	Weak transcription	Spleen	Spleen
10	chr17:16922400-16928000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:16922600-16925200	Weak transcription	Gastric	stomach
12	chr17:16922800-16928800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr17:16923400-16925400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:16923600-16926000	Enhancers	Right Ventricle	heart
15	chr17:16923600-16926800	Enhancers	Brain Anterior Caudate	brain
16	chr17:16923800-16925400	Weak transcription	Esophagus	oesophagus
17	chr17:16923800-16928200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:16923800-16929000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:16923800-16929000	Weak transcription	NHEK	skin
20	chr17:16924000-16925400	Enhancers	Adipose Nuclei	Adipose
21	chr17:16924000-16926000	Enhancers	Right Atrium	heart
22	chr17:16924000-16926600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr17:16924200-16924600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr17:16924200-16924600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:16924200-16924600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr17:16924200-16924600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:16924200-16924600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr17:16924200-16924600	Flanking Active TSS	HSMMtube	muscle
29	chr17:16924200-16924800	Flanking Active TSS	Fetal Intestine Large	intestine
30	chr17:16924200-16924800	Enhancers	K562	blood
31	chr17:16924200-16925000	Enhancers	Osteobl	bone
32	chr17:16924200-16925200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr17:16924200-16925200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr17:16924200-16925200	Enhancers	Duodenum Mucosa	Duodenum
35	chr17:16924200-16925200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr17:16924200-16925200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr17:16924200-16925200	Enhancers	Small Intestine	intestine
38	chr17:16924200-16925200	Enhancers	NHDF-Ad	bronchial
39	chr17:16924200-16925400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr17:16924200-16925400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:16924200-16925400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:16924200-16925400	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr17:16924200-16925400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr17:16924200-16925400	Enhancers	Fetal Lung	lung
45	chr17:16924200-16925400	Enhancers	Fetal Muscle Trunk	muscle
46	chr17:16924200-16925400	Flanking Active TSS	A549	lung
47	chr17:16924200-16925400	Enhancers	NH-A	brain
48	chr17:16924200-16925600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:16924200-16925600	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr17:16924200-16926000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links