Variant report

Variant	rs16852073
Chromosome Location	chr3:141764803-141764804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr3:141764720-141766662	K562	blood:	n/a	chr3:141765797-141765809 chr3:141765360-141765373 chr3:141765789-141765806 chr3:141765362-141765371 chr3:141765357-141765378
2	TEAD4	chr3:141764775-141766459	K562	blood:	n/a	n/a
3	NR2F2	chr3:141764792-141766211	K562	blood:	n/a	n/a
4	GATA1	chr3:141764783-141766394	PBDE	blood:	n/a	chr3:141765797-141765809 chr3:141765360-141765373 chr3:141765789-141765806 chr3:141765362-141765371 chr3:141765357-141765378

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141746178..141749439-chr3:141764015..141767847,4	K562	blood:
2	chr3:141743220..141745863-chr3:141763714..141765255,2	K562	blood:

Variant related genes	Relation type
ENSG00000233597	TF binding region
ENSG00000114126	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11569280	1.00[ASN][1000 genomes]
rs11569294	1.00[ASN][1000 genomes]
rs1355438	0.95[YRI][hapmap]
rs16852086	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs60029878	1.00[ASN][1000 genomes]
rs7616491	1.00[MEX][hapmap]
rs9877817	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers 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 target site	26 gene(s)	inside rSNPs	diseases
5	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv877553	chr3:141732321-141786073	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv877554	chr3:141735532-141781890	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv877555	chr3:141740076-141791408	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	esv2757013	chr3:141756541-142094631	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16852073	TFDP2	cis	multi-tissue	Pritchard
rs16852073	TFDP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141747600-141773000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:141747600-141780400	Weak transcription	Left Ventricle	heart
3	chr3:141751200-141765000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:141753600-141768400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:141755200-141771400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:141758400-141777400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:141758800-141768800	Weak transcription	Esophagus	oesophagus
8	chr3:141758800-141775800	Weak transcription	Ovary	ovary
9	chr3:141760000-141770000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:141760400-141773800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:141760600-141800800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:141760800-141772600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:141760800-141774600	Weak transcription	Liver	Liver
14	chr3:141761000-141772600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:141761000-141773400	Weak transcription	Dnd41	blood
16	chr3:141761000-141781600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:141761000-141807800	Weak transcription	Fetal Lung	lung
18	chr3:141761600-141772200	Weak transcription	Adipose Nuclei	Adipose
19	chr3:141761600-141775600	Weak transcription	NHEK	skin
20	chr3:141761800-141819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:141762000-141772800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:141762600-141775800	Weak transcription	Lung	lung
23	chr3:141762800-141782800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:141763000-141765200	Strong transcription	Fetal Thymus	thymus
25	chr3:141763000-141765200	Weak transcription	Thymus	Thymus
26	chr3:141763000-141765400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:141763000-141767400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:141763000-141770000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:141763000-141770000	Weak transcription	Fetal Stomach	stomach
30	chr3:141763000-141771400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:141763000-141772800	Weak transcription	Brain Germinal Matrix	brain
32	chr3:141763000-141775000	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:141763000-141778200	Weak transcription	Fetal Intestine Large	intestine
34	chr3:141763000-141820000	Weak transcription	Pancreas	Pancrea
35	chr3:141763000-141824200	Weak transcription	Aorta	Aorta
36	chr3:141763200-141767400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:141763600-141766600	Weak transcription	Fetal Intestine Small	intestine
38	chr3:141764000-141765400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:141764000-141825600	Weak transcription	Primary T cells from cord blood	blood
40	chr3:141764200-141765600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:141764400-141766600	Enhancers	Primary hematopoietic stem cells	blood
42	chr3:141764600-141765200	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr3:141764600-141766200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:141764600-141770000	Weak transcription	Psoas Muscle	Psoas
45	chr3:141764800-141765000	Enhancers	Primary B cells from cord blood	blood
46	chr3:141764800-141766400	Flanking Active TSS	K562	blood

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