Variant report

Variant	rs2204683
Chromosome Location	chr12:50522376-50522377
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50505960..50508490-chr12:50521019..50522677,2	MCF-7	breast:
2	chr12:50521333..50523123-chr12:50530434..50532715,2	K562	blood:
3	chr12:50521063..50523266-chr12:50526942..50528564,2	MCF-7	breast:
4	chr12:50503233..50504882-chr12:50521389..50523983,2	K562	blood:

Variant related genes	Relation type
ENSG00000178449	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10735824	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783338	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169278	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169281	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169282	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12369049	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369104	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12819883	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554844	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554845	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124432	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34167640	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741562	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59262224	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580728	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66782120	0.85[ASN][1000 genomes]
rs7135322	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138945	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294618	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307230	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307469	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308474	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398567	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7961065	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961112	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964698	0.86[EUR][1000 genomes]
rs7967979	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968119	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972465	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978904	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2204683	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs2204683	CERS5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50506800-50523600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
8	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
10	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:50509400-50522600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:50510800-50523800	Weak transcription	Psoas Muscle	Psoas
13	chr12:50510800-50528400	Strong transcription	Liver	Liver
14	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:50512600-50522800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:50512600-50529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
19	chr12:50514200-50522800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:50514800-50523600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:50515400-50522400	Weak transcription	K562	blood
22	chr12:50515600-50523800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:50515800-50523600	Weak transcription	HepG2	liver
24	chr12:50515800-50523800	Weak transcription	Fetal Brain Male	brain
25	chr12:50516000-50532400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:50516600-50536200	Strong transcription	Fetal Intestine Large	intestine
27	chr12:50517600-50523000	Weak transcription	Fetal Brain Female	brain
28	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:50518000-50522600	Weak transcription	Small Intestine	intestine
30	chr12:50518000-50523600	Weak transcription	Esophagus	oesophagus
31	chr12:50518000-50532400	Strong transcription	HSMM	muscle
32	chr12:50518600-50522600	Weak transcription	Hela-S3	cervix
33	chr12:50519200-50524000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:50519200-50538200	Strong transcription	Fetal Muscle Leg	muscle
35	chr12:50519400-50523600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr12:50519400-50525200	Strong transcription	Colon Smooth Muscle	Colon
37	chr12:50519400-50538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:50519600-50522600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:50519600-50525000	Strong transcription	Adipose Nuclei	Adipose
40	chr12:50519600-50532600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:50519600-50537800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:50519600-50538200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:50519800-50523400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr12:50519800-50523600	Weak transcription	Brain Substantia Nigra	brain
45	chr12:50520000-50522600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:50520000-50523800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:50520200-50529400	Strong transcription	Fetal Intestine Small	intestine
48	chr12:50520200-50537800	Strong transcription	Primary T cells from cord blood	blood
49	chr12:50520200-50539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:50520400-50523400	Strong transcription	Primary B cells from peripheral blood	blood

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