Variant report

Variant	rs2289769
Chromosome Location	chr12:46600494-46600495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46599272..46601027-chr12:46763701..46766006,2	MCF-7	breast:
2	chr12:46598504..46606384-chr12:46660159..46664661,13	MCF-7	breast:
3	chr12:46545467..46546982-chr12:46599241..46601124,2	MCF-7	breast:
4	chr12:46600082..46602843-chr20:56269478..56271257,2	MCF-7	breast:
5	chr12:46593719..46596069-chr12:46598625..46601594,2	K562	blood:
6	chr12:46598140..46600634-chr12:46609725..46611307,2	MCF-7	breast:
7	chr12:46598258..46600271-chr12:46600295..46602398,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10880935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11183394	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11608815	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11615731	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs12299972	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422328	0.87[EUR][1000 genomes]
rs1444590	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17096794	0.82[CHB][hapmap];1.00[AFR][1000 genomes]
rs61923106	0.90[ASN][1000 genomes]
rs6582621	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7977873	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7980700	0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754441	chr12:46590364-46605239	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46581600-46603200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr12:46582200-46603200	Weak transcription	Small Intestine	intestine
3	chr12:46587400-46602000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:46587400-46602000	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr12:46587400-46603000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:46587800-46601400	Strong transcription	HSMMtube	muscle
7	chr12:46588000-46603000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:46588200-46601200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:46588200-46601400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:46588200-46602200	Strong transcription	HUVEC	blood vessel
11	chr12:46588400-46601400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr12:46588400-46602200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:46588400-46602400	Strong transcription	HMEC	breast
14	chr12:46588600-46601400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:46588600-46602000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:46588600-46602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:46588600-46602800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:46588800-46601600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:46588800-46602000	Strong transcription	HepG2	liver
20	chr12:46588800-46602400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr12:46589000-46601400	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:46589000-46601600	Strong transcription	HSMM	muscle
23	chr12:46589400-46602400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr12:46589600-46603000	Strong transcription	NHEK	skin
25	chr12:46589800-46608400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:46590200-46601200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:46590600-46601200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:46590600-46601600	Strong transcription	Primary hematopoietic stem cells	blood
29	chr12:46590600-46601800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:46590600-46602000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:46590600-46603200	Weak transcription	Pancreas	Pancrea
32	chr12:46590600-46603200	Weak transcription	Right Atrium	heart
33	chr12:46590600-46603600	Weak transcription	Brain Angular Gyrus	brain
34	chr12:46590600-46603800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:46590800-46601400	Strong transcription	A549	lung
36	chr12:46590800-46601600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:46590800-46601600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:46590800-46603000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:46590800-46603200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:46590800-46613200	Strong transcription	Hela-S3	cervix
41	chr12:46591000-46601000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr12:46591000-46603200	Weak transcription	Lung	lung
43	chr12:46591000-46613200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:46591000-46613600	Weak transcription	Fetal Brain Male	brain
45	chr12:46591000-46613600	Weak transcription	Gastric	stomach
46	chr12:46591800-46603600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:46592000-46602200	Weak transcription	Brain Substantia Nigra	brain
48	chr12:46592400-46603000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr12:46592400-46603400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:46592400-46609800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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