Variant report

Variant	rs11130077
Chromosome Location	chr3:45877712-45877713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1129183	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs13065964	0.82[GIH][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap]
rs13318088	0.81[ASN][1000 genomes]
rs1386930	0.82[GIH][hapmap];0.87[LWK][hapmap];0.82[YRI][hapmap]
rs1488369	0.82[GIH][hapmap];0.87[LWK][hapmap];0.82[YRI][hapmap]
rs1488370	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883091	0.81[ASN][1000 genomes]
rs1883092	0.81[ASN][1000 genomes]
rs2286487	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2633734	0.81[ASN][1000 genomes]
rs2742364	0.81[ASN][1000 genomes]
rs2742365	0.81[ASN][1000 genomes]
rs3774643	0.81[ASN][1000 genomes]
rs3774644	0.81[ASN][1000 genomes]
rs45558831	0.81[ASN][1000 genomes]
rs4683143	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60103812	0.81[ASN][1000 genomes]
rs61157369	0.81[ASN][1000 genomes]
rs9823284	0.81[ASN][1000 genomes]
rs9830944	0.81[ASN][1000 genomes]
rs9844499	0.81[ASN][1000 genomes]
rs9868648	0.81[ASN][1000 genomes]
rs9882270	0.81[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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11130077	RNF123	cis	cerebellum	SCAN
rs11130077	CCDC71	cis	parietal	SCAN
rs11130077	SLC6A20	cis	cerebellum	SCAN
rs11130077	CCR1	cis	cerebellum	SCAN
rs11130077	CDC25A	cis	cerebellum	SCAN

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