Variant report

Variant	rs4930718
Chromosome Location	chr12:123913433-123913434
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	chr12:123912338..123913868-chr12:124018894..124020678,2	K562	blood:
2	chr12:123907694..123909490-chr12:123912059..123914448,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1060105	0.91[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs12298826	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs12316131	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs12322888	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs1402275	0.84[GIH][hapmap]
rs1716170	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs1716171	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs1879380	0.87[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs1969354	0.81[GIH][hapmap]
rs2337934	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs28376121	0.82[EUR][1000 genomes]
rs28406193	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs28410896	0.83[EUR][1000 genomes]
rs28458312	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs28472704	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs28481863	0.86[EUR][1000 genomes]
rs28569885	0.97[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs28625019	0.97[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28636834	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs28676499	0.88[EUR][1000 genomes]
rs28706696	0.97[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28715490	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4759371	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs4759415	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs4930719	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7953929	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4930718	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs4930718	RILPL2	cis	lymphoblastoid	seeQTL
rs4930718	PITPNM2	cis	cerebellum	SCAN
rs4930718	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs4930718	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs4930718	ANAPC5	cis	parietal	SCAN
rs4930718	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs4930718	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs4930718	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs4930718	CDK2AP1	cis	lymphoblastoid	seeQTL
rs4930718	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123889600-123917000	Weak transcription	K562	blood
2	chr12:123890800-123917200	Weak transcription	Fetal Kidney	kidney
3	chr12:123891200-123920400	Weak transcription	Psoas Muscle	Psoas
4	chr12:123891600-123919800	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:123891600-123920000	Weak transcription	Small Intestine	intestine
6	chr12:123892200-123916800	Weak transcription	NHEK	skin
7	chr12:123892200-123920200	Weak transcription	NH-A	brain
8	chr12:123892800-123920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:123893400-123918200	Weak transcription	Hela-S3	cervix
10	chr12:123894000-123920600	Weak transcription	HSMMtube	muscle
11	chr12:123894200-123917000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:123894200-123917000	Weak transcription	HUVEC	blood vessel
13	chr12:123894800-123920000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:123895200-123918200	Weak transcription	Pancreas	Pancrea
15	chr12:123895200-123920000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:123895200-123920000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:123895200-123920000	Weak transcription	HSMM	muscle
18	chr12:123895200-123920000	Weak transcription	NHLF	lung
19	chr12:123895200-123920200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:123895200-123920200	Weak transcription	A549	lung
21	chr12:123896200-123915600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:123896200-123915800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:123896400-123916200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:123899600-123916000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:123903200-123917200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:123905600-123916800	Weak transcription	HMEC	breast
27	chr12:123905800-123918200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:123907600-123915000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:123907600-123916800	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:123907600-123916800	Weak transcription	NHDF-Ad	bronchial
31	chr12:123907600-123917000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:123907600-123917200	Weak transcription	Gastric	stomach
33	chr12:123907600-123920000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:123907600-123920200	Weak transcription	Placenta	Placenta
35	chr12:123907600-123920200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:123907800-123920000	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:123908600-123918200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:123908600-123920200	Weak transcription	Fetal Intestine Small	intestine
39	chr12:123909800-123914800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:123910800-123913600	Strong transcription	Dnd41	blood
41	chr12:123910800-123915600	Strong transcription	Aorta	Aorta
42	chr12:123910800-123916000	Strong transcription	Adipose Nuclei	Adipose
43	chr12:123911200-123916000	Strong transcription	Fetal Stomach	stomach
44	chr12:123911200-123916200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:123911400-123915000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:123911400-123915600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr12:123911400-123916200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:123911400-123916200	Strong transcription	Lung	lung
49	chr12:123911600-123913600	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:123911600-123913600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links