Variant report

Variant	rs6801211
Chromosome Location	chr3:48774420-48774421
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	chr3:48774382..48777198-chr3:48777431..48780356,3	K562	blood:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10780033	0.82[YRI][hapmap]
rs10865953	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11130176	0.82[YRI][hapmap]
rs1134591	0.82[YRI][hapmap]
rs12493289	0.83[YRI][hapmap]
rs12632533	1.00[CEU][hapmap]
rs12715430	0.80[EUR][1000 genomes]
rs14018	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4858799	0.84[EUR][1000 genomes]
rs4858800	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4858830	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4974079	0.92[YRI][hapmap]
rs4974085	0.82[YRI][hapmap]
rs4974087	0.92[YRI][hapmap]
rs4974088	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6442129	0.84[EUR][1000 genomes]
rs6442130	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs6442131	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6446252	0.93[YRI][hapmap]
rs6446253	0.85[YRI][hapmap]
rs6766238	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6796790	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs7429596	0.91[EUR][1000 genomes]
rs7430501	0.82[YRI][hapmap]
rs7431857	0.82[YRI][hapmap]
rs7610519	0.85[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7627404	0.92[YRI][hapmap]
rs7639370	0.92[EUR][1000 genomes]
rs7641050	0.88[EUR][1000 genomes]
rs7653408	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9311430	0.82[YRI][hapmap]
rs9311431	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9311433	0.82[YRI][hapmap]
rs9637481	0.90[YRI][hapmap]
rs9682444	0.92[YRI][hapmap]
rs9755490	0.92[YRI][hapmap]
rs9835307	0.92[YRI][hapmap]
rs9848268	0.86[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9860187	0.81[YRI][hapmap]
rs9864243	0.80[EUR][1000 genomes]
rs9873227	0.98[EUR][1000 genomes]
rs9876848	0.92[YRI][hapmap]
rs9879978	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9882443	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9884022	0.82[YRI][hapmap]

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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6801211	AMT	cis	lung	GTEx
rs6801211	NCKIPSD	cis	Nerve Tibial	GTEx
rs6801211	AMT	cis	Artery Tibial	GTEx
rs6801211	NICN1-AS1	cis	Thyroid	GTEx
rs6801211	WDR6	cis	Muscle Skeletal	GTEx
rs6801211	QRICH1	cis	Nerve Tibial	GTEx
rs6801211	AMT	cis	Whole Blood	GTEx
rs6801211	WDR6	cis	Nerve Tibial	GTEx
rs6801211	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6801211	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6801211	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6801211	WDR6	cis	Heart Left Ventricle	GTEx
rs6801211	WDR6	cis	lung	GTEx
rs6801211	NICN1	cis	Thyroid	GTEx
rs6801211	AMT	cis	Nerve Tibial	GTEx
rs6801211	AMT	cis	Thyroid	GTEx
rs6801211	AMT	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48770800-48774600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr3:48771000-48776200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:48771200-48776000	Weak transcription	HMEC	breast
4	chr3:48772800-48777200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:48772800-48780200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:48773000-48776400	Weak transcription	NHEK	skin
7	chr3:48773200-48775000	Weak transcription	Fetal Lung	lung
8	chr3:48773200-48775000	Weak transcription	Left Ventricle	heart
9	chr3:48773200-48775000	Weak transcription	Stomach Mucosa	stomach
10	chr3:48773200-48775000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:48773200-48775600	Weak transcription	Placenta	Placenta
12	chr3:48773200-48776000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:48773200-48776000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:48773200-48777000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:48773200-48777000	Weak transcription	HSMMtube	muscle
16	chr3:48773200-48777200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:48773400-48774800	Weak transcription	Adipose Nuclei	Adipose
18	chr3:48773400-48775000	Weak transcription	Brain Anterior Caudate	brain
19	chr3:48773400-48775000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:48773400-48775000	Weak transcription	Fetal Stomach	stomach
21	chr3:48773400-48775200	Weak transcription	Fetal Intestine Large	intestine
22	chr3:48773400-48775800	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:48773400-48776200	Weak transcription	Colonic Mucosa	Colon
24	chr3:48773400-48776200	Weak transcription	Small Intestine	intestine
25	chr3:48773400-48776400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:48773400-48776800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:48773400-48777000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:48773400-48777000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:48773400-48777000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:48773600-48774800	Weak transcription	Liver	Liver
31	chr3:48773600-48774800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:48773600-48775000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:48773600-48775000	Weak transcription	Fetal Kidney	kidney
34	chr3:48773600-48776000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:48773600-48777200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:48773600-48777200	Weak transcription	NHDF-Ad	bronchial
37	chr3:48773800-48777000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:48774000-48777000	Enhancers	Duodenum Mucosa	Duodenum
39	chr3:48774200-48775000	Weak transcription	Fetal Intestine Small	intestine
40	chr3:48774200-48776400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:48774200-48777200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:48774400-48775000	Weak transcription	HepG2	liver

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