Variant report

Variant	rs9812360
Chromosome Location	chr3:49402351-49402352
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	chr3:49401040..49402958-chr3:49448886..49451002,2	K562	blood:
2	chr3:49399927..49402540-chr3:49449008..49451002,2	K562	blood:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10155014	0.85[EUR][1000 genomes]
rs11130190	0.91[EUR][1000 genomes]
rs11710434	0.81[EUR][1000 genomes]
rs11715060	0.81[EUR][1000 genomes]
rs11719762	0.90[EUR][1000 genomes]
rs11720542	0.81[EUR][1000 genomes]
rs11720657	0.91[EUR][1000 genomes]
rs13096474	0.85[EUR][1000 genomes]
rs1464569	0.82[EUR][1000 genomes]
rs2140270	0.86[EUR][1000 genomes]
rs2177268	0.86[EUR][1000 genomes]
rs3448	0.91[EUR][1000 genomes]
rs4955413	0.88[EUR][1000 genomes]
rs4955424	0.87[EUR][1000 genomes]
rs4955425	0.86[EUR][1000 genomes]
rs4955430	0.90[EUR][1000 genomes]
rs56127630	0.86[EUR][1000 genomes]
rs62259933	0.82[EUR][1000 genomes]
rs62259943	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62259944	0.84[EUR][1000 genomes]
rs62259947	0.86[EUR][1000 genomes]
rs6446262	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446275	0.82[EUR][1000 genomes]
rs6769744	0.90[EUR][1000 genomes]
rs6775069	0.92[EUR][1000 genomes]
rs6784203	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6785045	0.86[EUR][1000 genomes]
rs6796147	0.91[EUR][1000 genomes]
rs6805609	0.81[EUR][1000 genomes]
rs6809204	0.85[EUR][1000 genomes]
rs73088137	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7620024	0.84[EUR][1000 genomes]
rs7648995	0.86[EUR][1000 genomes]
rs8897	0.83[EUR][1000 genomes]
rs940045	0.84[EUR][1000 genomes]
rs974495	0.90[EUR][1000 genomes]
rs9817807	0.84[EUR][1000 genomes]
rs9842132	0.87[EUR][1000 genomes]
rs9847585	0.82[EUR][1000 genomes]
rs9860285	0.82[EUR][1000 genomes]
rs9861027	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv236940	chr3:49399471-49404775	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9812360	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9812360	AMT	cis	Artery Tibial	GTEx
rs9812360	AMT	cis	Whole Blood	GTEx
rs9812360	AMT	cis	Muscle Skeletal	GTEx
rs9812360	WDR6	cis	Nerve Tibial	GTEx
rs9812360	AMT	cis	Artery Aorta	GTEx
rs9812360	WDR6	cis	Muscle Skeletal	GTEx
rs9812360	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9812360	WDR6	cis	Esophagus Muscularis	GTEx
rs9812360	NICN1	cis	Thyroid	GTEx
rs9812360	AMT	cis	Esophagus Mucosa	GTEx
rs9812360	AMT	cis	Adipose Subcutaneous	GTEx
rs9812360	AMT	cis	lung	GTEx
rs9812360	AMT	cis	Thyroid	GTEx
rs9812360	NICN1-AS1	cis	Thyroid	GTEx
rs9812360	AMT	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396400-49413600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:49396400-49418600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49396600-49403600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:49396600-49406200	Strong transcription	Rectal Smooth Muscle	rectum
5	chr3:49396600-49410200	Weak transcription	Psoas Muscle	Psoas
6	chr3:49396600-49413200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:49396600-49413200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr3:49396600-49413800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:49396600-49414400	Weak transcription	Fetal Brain Male	brain
10	chr3:49396800-49404000	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:49396800-49406000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:49396800-49406000	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:49396800-49406200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr3:49396800-49408000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:49396800-49410800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:49396800-49412800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:49396800-49413200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:49396800-49413400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:49396800-49413400	Strong transcription	Thymus	Thymus
20	chr3:49396800-49413600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:49397000-49403400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:49397000-49406000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr3:49397000-49406200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:49397000-49406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:49397000-49408000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:49397000-49412800	Strong transcription	Lung	lung
28	chr3:49397000-49413000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49397000-49413200	Strong transcription	Adipose Nuclei	Adipose
30	chr3:49397000-49415200	Strong transcription	Fetal Stomach	stomach
31	chr3:49397200-49403600	Strong transcription	Left Ventricle	heart
32	chr3:49397200-49406000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:49397200-49406400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:49397200-49413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:49397200-49423800	Weak transcription	Fetal Heart	heart
36	chr3:49397400-49403800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:49397400-49410400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:49397400-49410600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:49397400-49411200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:49397400-49413200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:49397400-49413200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:49397400-49413400	Strong transcription	Fetal Intestine Large	intestine
43	chr3:49397400-49413400	Strong transcription	Fetal Muscle Leg	muscle
44	chr3:49397400-49413400	Strong transcription	Placenta	Placenta
45	chr3:49397400-49416400	Strong transcription	Fetal Intestine Small	intestine
46	chr3:49397600-49406000	Strong transcription	Liver	Liver
47	chr3:49397600-49413200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:49397600-49413200	Strong transcription	Spleen	Spleen
49	chr3:49397600-49413600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:49397800-49403600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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