Variant report

Variant	rs56773627
Chromosome Location	chr12:50417841-50417842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50416480..50418026-chr12:50426397..50428337,2	K562	blood:
2	chr12:50235029..50238212-chr12:50416884..50420841,4	K562	blood:
3	chr12:50410558..50416843-chr12:50417238..50421054,9	MCF-7	breast:
4	chr12:50415480..50418292-chr12:50448192..50450079,2	K562	blood:
5	chr12:50235029..50237749-chr12:50416744..50419038,3	K562	blood:
6	chr12:50416797..50419367-chr12:50793748..50795984,3	K562	blood:
7	chr12:50410622..50412312-chr12:50416219..50419390,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161813	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10219607	0.91[AMR][1000 genomes]
rs12313336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12313701	0.86[ASN][1000 genomes]
rs58424082	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61147017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73297484	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73297487	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73297491	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7972448	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][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	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
2	chr12:50383000-50418000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:50388200-50418000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:50391000-50418000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:50392800-50418200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:50399200-50418200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:50400400-50418200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:50400600-50418200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:50401200-50418200	Weak transcription	Primary B cells from cord blood	blood
10	chr12:50403000-50418600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:50407800-50418000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:50408400-50418000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:50409000-50418000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:50409200-50418000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:50409200-50418200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:50409200-50418400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:50409400-50418000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:50409800-50418400	Weak transcription	Primary T cells from cord blood	blood
19	chr12:50410000-50418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:50410200-50418200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:50410600-50418000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:50410600-50418000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:50410600-50418600	Weak transcription	Spleen	Spleen
24	chr12:50411200-50418200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:50411200-50418200	Weak transcription	Thymus	Thymus
26	chr12:50411200-50418600	Weak transcription	Small Intestine	intestine
27	chr12:50411400-50418000	Weak transcription	HMEC	breast
28	chr12:50411400-50418000	Weak transcription	NH-A	brain
29	chr12:50411400-50418200	Weak transcription	Brain Anterior Caudate	brain
30	chr12:50411400-50418200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:50411400-50418400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:50411400-50418400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:50411400-50418400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:50411600-50418000	Weak transcription	HUVEC	blood vessel
35	chr12:50411600-50418200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:50411800-50418200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:50411800-50418200	Weak transcription	Fetal Intestine Small	intestine
38	chr12:50411800-50418600	Weak transcription	Esophagus	oesophagus
39	chr12:50412000-50418600	Weak transcription	Lung	lung
40	chr12:50412400-50418000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:50412400-50418000	Weak transcription	Fetal Brain Female	brain
42	chr12:50412600-50418000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:50412600-50418400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:50413000-50418000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr12:50413000-50418000	Weak transcription	Fetal Stomach	stomach
46	chr12:50413000-50418600	Weak transcription	Stomach Mucosa	stomach
47	chr12:50413200-50418000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:50413200-50418200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:50413200-50418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:50413400-50418000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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