Variant report

Variant	rs56174413
Chromosome Location	chr3:141665145-141665146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141662334..141665277-chr3:141666881..141671768,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFDP2-5	chr3:141663270-141666233	ENSG00000269905.1

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10935445	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935446	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10935447	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11707100	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11711748	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11713023	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12494971	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12497112	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1808584	0.97[ASN][1000 genomes]
rs3762726	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4683412	0.90[ASN][1000 genomes]
rs745966	0.90[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56174413	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
2	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
6	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
8	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:141643000-141675800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:141643400-141671200	Weak transcription	Right Ventricle	heart
11	chr3:141644800-141678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:141646800-141668200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:141647000-141668400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:141647000-141669200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:141647200-141669400	Weak transcription	Primary B cells from cord blood	blood
16	chr3:141647400-141668200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:141647400-141670400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:141647600-141670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:141647800-141668200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:141647800-141670200	Weak transcription	Adipose Nuclei	Adipose
21	chr3:141648000-141670000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:141648000-141670800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:141659200-141696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:141659400-141668400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:141659400-141673800	Weak transcription	Brain Germinal Matrix	brain
26	chr3:141659400-141678400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:141659600-141669400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:141659600-141670400	Weak transcription	NH-A	brain
29	chr3:141659600-141670800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:141659600-141671200	Weak transcription	Pancreas	Pancrea
31	chr3:141659600-141671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:141659600-141674000	Weak transcription	NHLF	lung
33	chr3:141659600-141676000	Weak transcription	Fetal Heart	heart
34	chr3:141659600-141676400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:141659600-141678200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:141659600-141678200	Weak transcription	NHDF-Ad	bronchial
37	chr3:141659600-141678400	Weak transcription	A549	lung
38	chr3:141660000-141668400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:141660000-141670400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:141660000-141670800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:141660000-141673800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:141660000-141674200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:141660200-141670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:141660200-141670800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:141660400-141671200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:141660600-141670200	Weak transcription	Fetal Brain Male	brain
47	chr3:141660600-141698200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:141660800-141669400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:141660800-141670200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:141660800-141670400	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links