Variant report

Variant	rs2742362
Chromosome Location	chr3:45875149-45875150
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45755255..45757201-chr3:45873107..45875719,2	MCF-7	breast:
2	chr3:45641864..45644802-chr3:45873980..45875948,2	K562	blood:
3	chr3:45874395..45876649-chr3:45877009..45879060,2	K562	blood:

Variant related genes	Relation type
ENSG00000163818	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2191032	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2673059	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2742361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4683142	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4683144	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4683145	0.92[EUR][1000 genomes]
rs6441934	1.00[MKK][hapmap]
rs9843446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9856760	1.00[CEU][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2742362	SLC6A20	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45849400-45875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:45858000-45882600	Weak transcription	A549	lung
3	chr3:45858400-45881200	Strong transcription	Dnd41	blood
4	chr3:45860000-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:45860000-45882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:45860400-45875800	Weak transcription	Placenta	Placenta
7	chr3:45860400-45877400	Strong transcription	Liver	Liver
8	chr3:45860800-45875200	Weak transcription	Aorta	Aorta
9	chr3:45861000-45882400	Weak transcription	Small Intestine	intestine
10	chr3:45861000-45882400	Weak transcription	NHDF-Ad	bronchial
11	chr3:45861000-45882600	Weak transcription	Stomach Mucosa	stomach
12	chr3:45861000-45882600	Weak transcription	Hela-S3	cervix
13	chr3:45861200-45879600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr3:45861200-45882400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:45861200-45882600	Weak transcription	Right Ventricle	heart
16	chr3:45861400-45882200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:45861400-45882200	Weak transcription	Fetal Heart	heart
18	chr3:45861800-45882600	Weak transcription	NHLF	lung
19	chr3:45862000-45882800	Weak transcription	Psoas Muscle	Psoas
20	chr3:45862200-45879400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:45862200-45882600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:45862400-45879800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:45862400-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:45862600-45877400	Strong transcription	Adipose Nuclei	Adipose
25	chr3:45862600-45878400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:45862800-45878400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:45862800-45882400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:45863000-45876600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:45863200-45877200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:45863200-45878400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:45863200-45879600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:45863400-45882600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:45863600-45877000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:45863800-45875400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:45864000-45881000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:45864600-45882600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:45864800-45882600	Weak transcription	Colonic Mucosa	Colon
38	chr3:45865200-45882200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:45865800-45877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:45866000-45877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:45866200-45878400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:45866400-45877200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:45867400-45877200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:45867400-45879000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:45867600-45877200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:45867600-45878400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:45867600-45879600	Strong transcription	Fetal Intestine Large	intestine
48	chr3:45867600-45882600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:45868200-45876800	Strong transcription	Fetal Stomach	stomach
50	chr3:45868200-45877400	Strong transcription	Brain Inferior Temporal Lobe	brain

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