Variant report

Variant	rs2972457
Chromosome Location	chr19:38136001-38136002
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38134173..38137861-chr19:38186479..38189500,3	K562	blood:
2	chr19:38135258..38137073-chr19:38144772..38146380,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120784	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2927743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972457	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38121800-38139200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:38121800-38140600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:38123400-38138800	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:38123600-38140000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:38123600-38140800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:38123600-38141400	ZNF genes & repeats	Liver	Liver
7	chr19:38124600-38140800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:38124600-38142000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:38124800-38136400	ZNF genes & repeats	Fetal Lung	lung
10	chr19:38124800-38143200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:38124800-38144400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:38125000-38136800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
13	chr19:38125600-38143200	ZNF genes & repeats	A549	lung
14	chr19:38125800-38139600	ZNF genes & repeats	Colon Smooth Muscle	Colon
15	chr19:38125800-38140800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
16	chr19:38126000-38141400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:38126200-38143200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:38126400-38139400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr19:38127200-38144600	Weak transcription	Hela-S3	cervix
20	chr19:38129200-38138400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:38129200-38139600	Strong transcription	HSMM	muscle
22	chr19:38129600-38139000	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr19:38130000-38141600	Strong transcription	Osteobl	bone
24	chr19:38130400-38138400	Strong transcription	Brain Germinal Matrix	brain
25	chr19:38130400-38142200	ZNF genes & repeats	GM12878-XiMat	blood
26	chr19:38130600-38138000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:38130600-38139800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:38131000-38139200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr19:38131000-38141000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:38131200-38136800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:38131600-38136600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
32	chr19:38131600-38137000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:38131600-38139200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:38131600-38141200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:38131800-38138800	Strong transcription	Brain Anterior Caudate	brain
36	chr19:38131800-38139000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:38131800-38140600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr19:38132000-38138600	Strong transcription	Fetal Brain Male	brain
39	chr19:38132000-38138800	Strong transcription	HSMMtube	muscle
40	chr19:38132000-38139000	ZNF genes & repeats	Ovary	ovary
41	chr19:38132000-38139800	Strong transcription	Brain Cingulate Gyrus	brain
42	chr19:38132200-38137400	Strong transcription	Fetal Intestine Large	intestine
43	chr19:38132200-38139000	Strong transcription	Placenta	Placenta
44	chr19:38132200-38139200	Strong transcription	Brain Angular Gyrus	brain
45	chr19:38132200-38139400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr19:38132400-38137400	Strong transcription	Thymus	Thymus
47	chr19:38132400-38138800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr19:38132400-38139000	Strong transcription	Fetal Thymus	thymus
49	chr19:38132400-38139200	Strong transcription	Brain Substantia Nigra	brain
50	chr19:38132400-38139400	Strong transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links