Variant report

Variant	rs2306390
Chromosome Location	chr12:58002599-58002600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57912257..57915408-chr12:58000825..58006358,4	K562	blood:
2	chr12:57930705..57935401-chr12:58001977..58005950,4	K562	blood:
3	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
4	chr12:57939583..57941703-chr12:58002111..58004794,2	K562	blood:

Variant related genes	Relation type
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175203	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10876994	0.82[CEU][hapmap]
rs11533604	0.83[EUR][1000 genomes]
rs11536137	0.83[EUR][1000 genomes]
rs11537654	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1545783	0.84[JPT][hapmap]
rs2888334	0.82[CEU][hapmap]
rs4760158	0.84[JPT][hapmap]
rs73123375	0.82[EUR][1000 genomes]
rs775251	0.82[CEU][hapmap]

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	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2306390	ESPL1	cis	parietal	SCAN
rs2306390	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs2306390	XRCC6BP1	cis	cerebellum	SCAN
rs2306390	RDH5	cis	cerebellum	SCAN
rs2306390	DKFZP586D0919	cis	multi-tissue	Pritchard
rs2306390	FAM119B	cis	cerebellum	SCAN
rs2306390	STAT6	cis	cerebellum	SCAN
rs2306390	TSPAN31	cis	parietal	SCAN
rs2306390	ITGB7	cis	cerebellum	SCAN
rs2306390	TSPAN31	cis	cerebellum	SCAN
rs2306390	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs2306390	METTL21B	cis	Adipose Subcutaneous	GTEx
rs2306390	FAM119B	cis	lymphoblastoid	seeQTL
rs2306390	CDK4	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57999400-58004000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:57999400-58004000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:57999400-58004800	Weak transcription	Gastric	stomach
4	chr12:57999600-58002600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:57999600-58002600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:57999600-58003800	Weak transcription	Aorta	Aorta
7	chr12:57999600-58004000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:57999600-58004200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:57999600-58004200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:57999600-58004200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:57999600-58004200	Weak transcription	NH-A	brain
12	chr12:57999600-58004200	Weak transcription	NHLF	lung
13	chr12:57999600-58004600	Weak transcription	GM12878-XiMat	blood
14	chr12:57999800-58002800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:57999800-58002800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:57999800-58002800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:57999800-58003200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:57999800-58003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:57999800-58003800	Weak transcription	Colonic Mucosa	Colon
20	chr12:57999800-58003800	Weak transcription	Right Atrium	heart
21	chr12:57999800-58004000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:57999800-58004000	Weak transcription	NHDF-Ad	bronchial
23	chr12:57999800-58004000	Weak transcription	Osteobl	bone
24	chr12:57999800-58004200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:57999800-58004200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:57999800-58004200	Weak transcription	Pancreas	Pancrea
27	chr12:57999800-58004600	Weak transcription	A549	lung
28	chr12:57999800-58004800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:57999800-58004800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:58000000-58002800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:58000000-58003000	Weak transcription	Fetal Kidney	kidney
32	chr12:58000000-58003400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:58000000-58003800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:58000000-58003800	Weak transcription	Fetal Brain Male	brain
35	chr12:58000000-58004200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:58000000-58004200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:58000200-58002600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:58000200-58002800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:58000200-58003000	Genic enhancers	Fetal Muscle Leg	muscle
40	chr12:58000200-58003200	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr12:58000200-58003400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:58000200-58003400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:58000200-58003400	Strong transcription	Thymus	Thymus
44	chr12:58000400-58002600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:58000400-58002600	Strong transcription	Brain Anterior Caudate	brain
46	chr12:58000400-58002800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:58000400-58003000	Weak transcription	Fetal Heart	heart
48	chr12:58000400-58003000	Strong transcription	Fetal Intestine Small	intestine
49	chr12:58000400-58003400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:58000400-58003400	Strong transcription	Fetal Brain Female	brain

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