Variant report

Variant	rs6766238
Chromosome Location	chr3:48801929-48801930
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	chr3:48800799..48802746-chr3:48804382..48806917,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 34 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10865953	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs11707968	0.82[EUR][1000 genomes]
rs12632533	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs12715430	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs14018	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4858799	0.83[EUR][1000 genomes]
rs4858800	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs4858830	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4974083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6442129	0.83[EUR][1000 genomes]
rs6442131	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6796790	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7429596	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7610519	0.85[EUR][1000 genomes]
rs7611628	0.81[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7639370	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7641050	0.85[EUR][1000 genomes]
rs7653408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9311431	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9848268	0.84[EUR][1000 genomes]
rs9859473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9864243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs9873227	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9879978	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9882443	1.00[CEU][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs990211	0.82[CEU][hapmap]

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	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
2	esv3407876	chr3:48774454-48823998	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs6766238	AMT	cis	lung	GTEx
rs6766238	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6766238	NICN1	cis	parietal	SCAN
rs6766238	LZTFL1	cis	cerebellum	SCAN
rs6766238	P4HTM	cis	lung	GTEx
rs6766238	ZNF589	cis	parietal	SCAN
rs6766238	AMT	cis	parietal	SCAN
rs6766238	WDR6	cis	parietal	SCAN
rs6766238	AMT	cis	Artery Aorta	GTEx
rs6766238	P4HTM	cis	parietal	SCAN
rs6766238	GPX1	cis	parietal	SCAN
rs6766238	NCKIPSD	cis	parietal	SCAN
rs6766238	AMT	cis	cerebellum	SCAN
rs6766238	NICN1-AS1	cis	Thyroid	GTEx
rs6766238	NCKIPSD	cis	Nerve Tibial	GTEx
rs6766238	AMT	cis	lymphoblastoid	seeQTL
rs6766238	AMT	cis	Adipose Subcutaneous	GTEx
rs6766238	WDR6	cis	Muscle Skeletal	GTEx
rs6766238	DALRD3	cis	cerebellum	SCAN
rs6766238	PHF7	cis	parietal	SCAN
rs6766238	NICN1	cis	cerebellum	SCAN
rs6766238	NICN1	cis	Thyroid	GTEx
rs6766238	WDR6	cis	cerebellum	SCAN
rs6766238	QRICH1	cis	cerebellum	SCAN
rs6766238	ARIH2	cis	Thyroid	GTEx
rs6766238	TLR9	cis	parietal	SCAN
rs6766238	AMT	cis	Artery Tibial	GTEx
rs6766238	AMT	cis	Nerve Tibial	GTEx
rs6766238	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6766238	DALRD3	cis	parietal	SCAN
rs6766238	WDR6	cis	Nerve Tibial	GTEx
rs6766238	AMT	cis	Thyroid	GTEx
rs6766238	IQCF1	cis	cerebellum	SCAN
rs6766238	AMT	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48777800-48807400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:48778000-48807200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:48778200-48814400	Weak transcription	Fetal Heart	heart
4	chr3:48778200-48820200	Weak transcription	Fetal Kidney	kidney
5	chr3:48778200-48836600	Weak transcription	A549	lung
6	chr3:48778600-48826000	Weak transcription	Stomach Mucosa	stomach
7	chr3:48782200-48814400	Weak transcription	K562	blood
8	chr3:48783400-48811400	Strong transcription	Fetal Stomach	stomach
9	chr3:48785400-48819200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:48786000-48803400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:48786200-48812600	Strong transcription	Fetal Muscle Leg	muscle
12	chr3:48786600-48807600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:48786600-48812800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:48786800-48807400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:48789200-48807400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:48789400-48807200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:48789400-48808000	Weak transcription	HUVEC	blood vessel
18	chr3:48789400-48844000	Weak transcription	Fetal Lung	lung
19	chr3:48789600-48820200	Weak transcription	Fetal Brain Male	brain
20	chr3:48789600-48820400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:48789600-48825800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:48789800-48807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:48789800-48807200	Weak transcription	Esophagus	oesophagus
24	chr3:48789800-48807200	Weak transcription	Spleen	Spleen
25	chr3:48789800-48807400	Weak transcription	Aorta	Aorta
26	chr3:48789800-48807400	Weak transcription	Right Ventricle	heart
27	chr3:48789800-48819000	Weak transcription	Small Intestine	intestine
28	chr3:48790000-48807200	Weak transcription	Gastric	stomach
29	chr3:48790000-48819600	Weak transcription	NHLF	lung
30	chr3:48790200-48807400	Weak transcription	NHEK	skin
31	chr3:48790200-48823600	Weak transcription	HMEC	breast
32	chr3:48790400-48807400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:48790600-48807600	Weak transcription	GM12878-XiMat	blood
34	chr3:48791200-48825800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:48792200-48804000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr3:48792800-48804800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:48793200-48825800	Weak transcription	Fetal Thymus	thymus
38	chr3:48794400-48807600	Weak transcription	NH-A	brain
39	chr3:48794600-48803600	Weak transcription	Brain Substantia Nigra	brain
40	chr3:48794600-48807400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:48794600-48811800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:48794800-48810200	Weak transcription	Hela-S3	cervix
43	chr3:48794800-48819600	Weak transcription	NHDF-Ad	bronchial
44	chr3:48795200-48819600	Weak transcription	Colonic Mucosa	Colon
45	chr3:48795200-48833600	Weak transcription	Psoas Muscle	Psoas
46	chr3:48795400-48802600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:48796400-48802600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:48796400-48804200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:48797000-48823400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:48797200-48807400	Weak transcription	HSMMtube	muscle

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