Variant report

Variant	rs6446262
Chromosome Location	chr3:49401153-49401154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49401040..49402958-chr3:49448886..49451002,2	K562	blood:
2	chr3:49399927..49402540-chr3:49449008..49451002,2	K562	blood:
3	chr3:49399346..49401429-chr3:49449633..49451334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1009051	0.82[EUR][1000 genomes]
rs10155014	0.92[EUR][1000 genomes]
rs1106620	0.85[EUR][1000 genomes]
rs11130190	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11710434	0.88[EUR][1000 genomes]
rs11715060	0.88[EUR][1000 genomes]
rs11719762	0.98[EUR][1000 genomes]
rs11720542	0.88[EUR][1000 genomes]
rs11720657	0.99[EUR][1000 genomes]
rs13096474	0.92[EUR][1000 genomes]
rs1464569	0.89[EUR][1000 genomes]
rs2140270	0.93[EUR][1000 genomes]
rs2177268	0.93[EUR][1000 genomes]
rs2329025	0.84[EUR][1000 genomes]
rs3448	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3870339	0.82[EUR][1000 genomes]
rs4855858	0.82[EUR][1000 genomes]
rs4855869	0.81[EUR][1000 genomes]
rs4955413	0.94[EUR][1000 genomes]
rs4955424	0.94[EUR][1000 genomes]
rs4955425	0.94[EUR][1000 genomes]
rs4955430	0.98[EUR][1000 genomes]
rs56127630	0.93[EUR][1000 genomes]
rs57273516	0.84[EUR][1000 genomes]
rs62259933	0.89[EUR][1000 genomes]
rs62259943	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62259944	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62259947	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62261183	0.83[EUR][1000 genomes]
rs6446275	0.89[EUR][1000 genomes]
rs6769744	0.98[EUR][1000 genomes]
rs6775069	0.99[EUR][1000 genomes]
rs6783003	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6784203	0.94[EUR][1000 genomes]
rs6785045	0.93[EUR][1000 genomes]
rs6790105	0.85[EUR][1000 genomes]
rs6796147	0.96[EUR][1000 genomes]
rs6805609	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6809204	0.92[EUR][1000 genomes]
rs72934271	0.83[EUR][1000 genomes]
rs73088137	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7355800	0.83[EUR][1000 genomes]
rs7374731	0.81[EUR][1000 genomes]
rs7613491	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7619789	0.84[EUR][1000 genomes]
rs7620024	0.91[EUR][1000 genomes]
rs7638750	0.86[EUR][1000 genomes]
rs7644148	0.80[EUR][1000 genomes]
rs7647973	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7648995	0.93[EUR][1000 genomes]
rs7651372	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8897	0.90[EUR][1000 genomes]
rs940045	0.91[EUR][1000 genomes]
rs9654010	0.81[EUR][1000 genomes]
rs974495	0.98[EUR][1000 genomes]
rs9809237	0.81[EUR][1000 genomes]
rs9812360	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9817807	0.91[EUR][1000 genomes]
rs9834535	0.81[EUR][1000 genomes]
rs9842132	0.94[EUR][1000 genomes]
rs9847585	0.85[EUR][1000 genomes]
rs9860055	0.86[EUR][1000 genomes]
rs9860285	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861027	0.93[EUR][1000 genomes]
rs9881860	0.84[AMR][1000 genomes];0.87[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6446262	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs6446262	AMT	cis	Muscle Skeletal	GTEx
rs6446262	WDR6	cis	Nerve Tibial	GTEx
rs6446262	NICN1-AS1	cis	Thyroid	GTEx
rs6446262	AMT	cis	Thyroid	GTEx
rs6446262	AMT	cis	Esophagus Muscularis	GTEx
rs6446262	ARIH2	cis	Thyroid	GTEx
rs6446262	NICN1	cis	Thyroid	GTEx
rs6446262	AMT	cis	Whole Blood	GTEx
rs6446262	AMT	cis	Artery Aorta	GTEx
rs6446262	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs6446262	WDR6	cis	Muscle Skeletal	GTEx
rs6446262	AMT	cis	Nerve Tibial	GTEx
rs6446262	AMT	cis	Esophagus Mucosa	GTEx
rs6446262	AMT	cis	Adipose Subcutaneous	GTEx
rs6446262	AMT	cis	Artery Tibial	GTEx
rs6446262	AMT	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396400-49401600	Genic enhancers	Osteobl	bone
2	chr3:49396400-49413600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:49396400-49418600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:49396600-49401400	Strong transcription	Primary B cells from cord blood	blood
5	chr3:49396600-49401400	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr3:49396600-49401600	Strong transcription	Colon Smooth Muscle	Colon
7	chr3:49396600-49403600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:49396600-49406200	Strong transcription	Rectal Smooth Muscle	rectum
9	chr3:49396600-49410200	Weak transcription	Psoas Muscle	Psoas
10	chr3:49396600-49413200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:49396600-49413200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr3:49396600-49413800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:49396600-49414400	Weak transcription	Fetal Brain Male	brain
14	chr3:49396800-49401800	Strong transcription	Esophagus	oesophagus
15	chr3:49396800-49401800	Strong transcription	Fetal Lung	lung
16	chr3:49396800-49404000	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:49396800-49406000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:49396800-49406000	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:49396800-49406200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr3:49396800-49408000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:49396800-49410800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:49396800-49412800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:49396800-49413200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:49396800-49413400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:49396800-49413400	Strong transcription	Thymus	Thymus
26	chr3:49396800-49413600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:49397000-49401600	Strong transcription	Brain Anterior Caudate	brain
29	chr3:49397000-49401600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:49397000-49401800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:49397000-49402000	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:49397000-49403400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:49397000-49406000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr3:49397000-49406200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:49397000-49406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:49397000-49408000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:49397000-49412800	Strong transcription	Lung	lung
38	chr3:49397000-49413000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:49397000-49413200	Strong transcription	Adipose Nuclei	Adipose
40	chr3:49397000-49415200	Strong transcription	Fetal Stomach	stomach
41	chr3:49397200-49401400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr3:49397200-49401600	Strong transcription	Brain Germinal Matrix	brain
43	chr3:49397200-49401600	Strong transcription	Pancreas	Pancrea
44	chr3:49397200-49401600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:49397200-49401800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:49397200-49403600	Strong transcription	Left Ventricle	heart
47	chr3:49397200-49406000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:49397200-49406400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:49397200-49413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:49397200-49423800	Weak transcription	Fetal Heart	heart

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