Variant report

Variant	rs2742364
Chromosome Location	chr3:45877888-45877889
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	chr3:45877879..45880836-chr3:45881346..45883533,3	K562	blood:

Variant related genes	Relation type
ENSG00000163818	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11130077	0.81[ASN][1000 genomes]
rs1129183	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318088	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488370	0.81[ASN][1000 genomes]
rs1883091	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286487	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531756	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2633734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774644	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45558831	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683143	0.96[ASN][1000 genomes]
rs60103812	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61157369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844499	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849511	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868648	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882270	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45858000-45882600	Weak transcription	A549	lung
2	chr3:45858400-45881200	Strong transcription	Dnd41	blood
3	chr3:45860000-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:45860000-45882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:45861000-45882400	Weak transcription	Small Intestine	intestine
6	chr3:45861000-45882400	Weak transcription	NHDF-Ad	bronchial
7	chr3:45861000-45882600	Weak transcription	Stomach Mucosa	stomach
8	chr3:45861000-45882600	Weak transcription	Hela-S3	cervix
9	chr3:45861200-45879600	Strong transcription	Stomach Smooth Muscle	stomach
10	chr3:45861200-45882400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:45861200-45882600	Weak transcription	Right Ventricle	heart
12	chr3:45861400-45882200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:45861400-45882200	Weak transcription	Fetal Heart	heart
14	chr3:45861800-45882600	Weak transcription	NHLF	lung
15	chr3:45862000-45882800	Weak transcription	Psoas Muscle	Psoas
16	chr3:45862200-45879400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:45862200-45882600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:45862400-45879800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:45862400-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:45862600-45878400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:45862800-45878400	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:45862800-45882400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:45863200-45878400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:45863200-45879600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:45863400-45882600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:45864000-45881000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:45864600-45882600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:45864800-45882600	Weak transcription	Colonic Mucosa	Colon
29	chr3:45865200-45882200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:45866200-45878400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:45867400-45879000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:45867600-45878400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:45867600-45879600	Strong transcription	Fetal Intestine Large	intestine
34	chr3:45867600-45882600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:45868400-45878600	Strong transcription	Brain Anterior Caudate	brain
36	chr3:45868600-45882400	Weak transcription	Fetal Brain Male	brain
37	chr3:45868600-45882400	Weak transcription	NHEK	skin
38	chr3:45868800-45882400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:45868800-45882600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:45870400-45882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:45870400-45882800	Weak transcription	Gastric	stomach
42	chr3:45870800-45882400	Weak transcription	HMEC	breast
43	chr3:45870800-45882600	Weak transcription	K562	blood
44	chr3:45871400-45879400	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:45871600-45878600	Strong transcription	Primary T cells from cord blood	blood
46	chr3:45871600-45879200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:45871800-45878400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:45871800-45879400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr3:45872400-45879000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:45872400-45881600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links