Variant report

Variant	rs3936179
Chromosome Location	chr12:48543584-48543585
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48321332..48322947-chr12:48541459..48543694,2	K562	blood:
2	chr12:48536767..48541851-chr12:48541890..48543935,4	MCF-7	breast:
3	chr12:48541868..48544385-chr12:48549459..48551114,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004746	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1004806	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10506277	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12301562	0.83[EUR][1000 genomes]
rs17224674	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17225261	0.89[AMR][1000 genomes]
rs17225366	0.89[AMR][1000 genomes]
rs17225751	0.89[AMR][1000 genomes]
rs17607800	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17824200	0.89[AMR][1000 genomes]
rs2228501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41291959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41291961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55682541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55707383	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs55752728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55794326	0.89[AMR][1000 genomes]
rs55886138	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55890195	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55894137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55945889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55953382	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56049209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56116946	0.89[AMR][1000 genomes]
rs56187356	0.93[EUR][1000 genomes]
rs56205628	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56288528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56378908	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60209369	0.83[EUR][1000 genomes]
rs74089155	0.93[EUR][1000 genomes]
rs74089159	0.82[EUR][1000 genomes]
rs74089163	0.82[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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3936179	ZNF641	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
5	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
10	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:48520000-48545600	Strong transcription	Hela-S3	cervix
17	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
18	chr12:48523400-48546600	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:48523800-48547400	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:48525600-48546200	Strong transcription	A549	lung
21	chr12:48526200-48547600	Strong transcription	Adipose Nuclei	Adipose
22	chr12:48526400-48543600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:48530200-48547600	Strong transcription	Placenta	Placenta
24	chr12:48531000-48546400	Strong transcription	Brain Angular Gyrus	brain
25	chr12:48531000-48547400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:48531000-48547800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:48531200-48547400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:48531200-48547400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr12:48531200-48547400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:48531200-48547400	Strong transcription	Fetal Intestine Large	intestine
31	chr12:48531200-48547600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:48531200-48547600	Strong transcription	HMEC	breast
33	chr12:48531200-48547800	Strong transcription	Primary T cells from cord blood	blood
34	chr12:48531200-48547800	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr12:48531200-48547800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr12:48531200-48548000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:48531400-48547400	Strong transcription	Colonic Mucosa	Colon
38	chr12:48531400-48548000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:48531600-48547200	Strong transcription	Brain Hippocampus Middle	brain
40	chr12:48531600-48547400	Strong transcription	Lung	lung
41	chr12:48531600-48547800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:48532200-48545600	Strong transcription	Aorta	Aorta
43	chr12:48532200-48548400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:48533000-48547400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:48533000-48547800	Strong transcription	Liver	Liver
46	chr12:48533200-48546200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:48533200-48547600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:48533200-48547800	Strong transcription	Fetal Thymus	thymus
49	chr12:48533600-48547400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:48533600-48548400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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