Variant report

Variant	rs17784714
Chromosome Location	chr3:47511698-47511699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47506187..47509677-chr3:47510013..47512919,3	K562	blood:
2	chr3:47510437..47514442-chr3:47515301..47518815,8	K562	blood:

Variant related genes	Relation type
ENSG00000114650	Chromatin interaction
ENSG00000238350	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11707038	0.84[EUR][1000 genomes]
rs34622620	1.00[ASN][1000 genomes]
rs41290656	1.00[ASN][1000 genomes]
rs4858816	0.95[EUR][1000 genomes]
rs62246470	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62248950	0.87[AMR][1000 genomes]
rs62260708	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62260713	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800588	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081211	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv3806	chr3:47488784-47518133	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv1816532	chr3:47490712-47511698	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1841538	chr3:47490712-47511698	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1848062	chr3:47490712-47511698	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1849930	chr3:47490712-47511698	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17784714	C3orf75	cis	cerebellum	SCAN
rs17784714	IFRD2	cis	parietal	SCAN
rs17784714	QRICH1	cis	parietal	SCAN
rs17784714	HYAL2	cis	cerebellum	SCAN
rs17784714	PRKAR2A	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47484600-47514000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:47484600-47514200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr3:47484600-47514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:47484600-47514200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:47484600-47514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:47484800-47514800	Weak transcription	Thymus	Thymus
8	chr3:47485000-47514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:47486000-47516000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:47486000-47516000	Weak transcription	Small Intestine	intestine
11	chr3:47486000-47516000	Weak transcription	HSMM	muscle
12	chr3:47486200-47516000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:47494600-47514000	Weak transcription	Esophagus	oesophagus
14	chr3:47494600-47514000	Weak transcription	Pancreas	Pancrea
15	chr3:47495400-47514600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:47497800-47514800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:47497800-47514800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:47497800-47514800	Weak transcription	Hela-S3	cervix
19	chr3:47497800-47516000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:47497800-47516000	Weak transcription	A549	lung
21	chr3:47497800-47516000	Weak transcription	NHDF-Ad	bronchial
22	chr3:47498800-47516000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:47499200-47514200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:47501000-47516200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:47501400-47516200	Weak transcription	HSMMtube	muscle
26	chr3:47502400-47516000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:47502800-47514800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:47502800-47515400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:47503200-47516000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:47503400-47516000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:47504000-47516200	Weak transcription	Gastric	stomach
32	chr3:47504400-47514000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:47504800-47514600	Weak transcription	Primary T cells from cord blood	blood
34	chr3:47504800-47514800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:47504800-47514800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:47504800-47515000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:47505000-47514600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:47505000-47514800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:47505000-47514800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:47505000-47515000	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:47505000-47516000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:47505200-47514200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:47505200-47514200	Weak transcription	Left Ventricle	heart
44	chr3:47505400-47514200	Weak transcription	Ovary	ovary
45	chr3:47505600-47516000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:47506800-47514200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:47506800-47516200	Weak transcription	Fetal Lung	lung
48	chr3:47507200-47514800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:47507200-47515000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:47507200-47516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links