Variant report

Variant	rs73299539
Chromosome Location	chr12:50466849-50466850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50465226..50467523-chr12:50469793..50471990,2	K562	blood:
2	chr12:50465539..50467962-chr12:50472151..50474107,2	K562	blood:
3	chr12:50259278..50261065-chr12:50464788..50467159,2	K562	blood:
4	chr12:50452539..50455408-chr12:50466138..50467868,2	MCF-7	breast:
5	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
6	chr12:50359856..50363195-chr12:50464299..50467277,4	MCF-7	breast:
7	chr12:50464486..50466222-chr12:50466787..50469329,2	K562	blood:

Variant related genes	Relation type
ENSG00000066117	Chromatin interaction
ENSG00000086159	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs57777059	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61731226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73299544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50460600-50469200	Weak transcription	Psoas Muscle	Psoas
3	chr12:50460600-50469400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50460800-50469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:50461000-50468800	Weak transcription	HSMMtube	muscle
6	chr12:50464000-50467000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:50464400-50467400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:50464400-50467600	Weak transcription	HepG2	liver
9	chr12:50464400-50468800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:50464400-50469200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:50464400-50469200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:50464400-50469200	Weak transcription	Fetal Lung	lung
13	chr12:50464400-50469200	Weak transcription	Pancreas	Pancrea
14	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
15	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
16	chr12:50464600-50467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:50464600-50468800	Weak transcription	Liver	Liver
18	chr12:50464600-50469200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:50464600-50469600	Weak transcription	Colonic Mucosa	Colon
20	chr12:50464800-50468600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:50464800-50468600	Weak transcription	Fetal Intestine Large	intestine
22	chr12:50464800-50468800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:50464800-50468800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:50464800-50468800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:50464800-50468800	Weak transcription	Fetal Intestine Small	intestine
26	chr12:50464800-50468800	Weak transcription	Gastric	stomach
27	chr12:50464800-50468800	Weak transcription	Right Ventricle	heart
28	chr12:50464800-50468800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:50464800-50468800	Weak transcription	NH-A	brain
30	chr12:50464800-50469000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:50464800-50469000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:50464800-50469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:50464800-50469000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:50464800-50469000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:50464800-50469000	Weak transcription	Stomach Mucosa	stomach
36	chr12:50464800-50469200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:50464800-50469200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:50464800-50469200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:50464800-50469200	Weak transcription	Brain Angular Gyrus	brain
40	chr12:50464800-50469200	Weak transcription	Brain Anterior Caudate	brain
41	chr12:50464800-50469200	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:50464800-50469200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:50464800-50469200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr12:50464800-50469200	Weak transcription	HMEC	breast
45	chr12:50464800-50471600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:50464800-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:50464800-50478200	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:50464800-50478200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:50464800-50478200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:50464800-50478400	Weak transcription	Primary T cells from cord blood	blood

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