Variant report

Variant	rs12895072
Chromosome Location	chr14:56168499-56168500
allele	C/T
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:25)

rs_ID	r²[population]
rs10444721	0.90[JPT][hapmap]
rs10483644	0.90[JPT][hapmap]
rs12432887	0.90[JPT][hapmap]
rs12434554	0.97[ASN][1000 genomes]
rs12435643	0.90[JPT][hapmap]
rs12587735	0.90[JPT][hapmap]
rs12590388	0.90[JPT][hapmap]
rs12590936	0.90[JPT][hapmap]
rs12888809	0.94[JPT][hapmap]
rs12893162	0.85[JPT][hapmap]
rs17128552	1.00[MEX][hapmap]
rs17128657	0.90[JPT][hapmap]
rs17128684	0.90[JPT][hapmap]
rs1951887	0.90[JPT][hapmap]
rs1951889	0.90[JPT][hapmap]
rs2252189	0.90[JPT][hapmap]
rs2274076	0.89[JPT][hapmap]
rs2274078	0.89[JPT][hapmap]
rs2296182	0.89[JPT][hapmap]
rs34062701	1.00[AFR][1000 genomes]
rs3765515	0.90[JPT][hapmap]
rs4357856	0.94[AFR][1000 genomes]
rs6573053	0.90[JPT][hapmap]
rs6573054	0.90[JPT][hapmap]
rs7156566	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832804	chr14:56083850-56277632	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv901966	chr14:56160904-56436203	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12895072	GCH1	cis	cerebellum	SCAN
rs12895072	KTN1	cis	cerebellum	SCAN
rs12895072	MAPK1IP1L	cis	cerebellum	SCAN
rs12895072	GCH1	cis	parietal	SCAN
rs12895072	KTN1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
2	chr14:56147400-56170400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:56148000-56174000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:56153400-56174000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr14:56153800-56170600	Weak transcription	Fetal Stomach	stomach
6	chr14:56153800-56172000	Weak transcription	Esophagus	oesophagus
7	chr14:56153800-56172400	Weak transcription	Dnd41	blood
8	chr14:56153800-56173800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:56153800-56174000	Weak transcription	Brain Anterior Caudate	brain
10	chr14:56154000-56172400	Weak transcription	Lung	lung
11	chr14:56154000-56173800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr14:56154000-56177800	Weak transcription	Left Ventricle	heart
13	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
14	chr14:56154400-56177800	Weak transcription	Fetal Muscle Leg	muscle
15	chr14:56154800-56174000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:56155600-56173600	Weak transcription	Primary T cells from cord blood	blood
17	chr14:56157600-56172400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr14:56157600-56178000	Weak transcription	Psoas Muscle	Psoas
19	chr14:56157600-56180000	Weak transcription	Primary B cells from cord blood	blood
20	chr14:56157800-56172200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr14:56162800-56174000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr14:56164600-56179600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:56166000-56172200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr14:56166200-56168800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr14:56166200-56169000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr14:56166200-56173800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:56166400-56172800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr14:56166400-56173600	Weak transcription	NHLF	lung
29	chr14:56166600-56171800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:56167200-56168800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:56167200-56169600	Weak transcription	HSMMtube	muscle
32	chr14:56167800-56168600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr14:56167800-56169600	Enhancers	GM12878-XiMat	blood
34	chr14:56168000-56169200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr14:56168000-56169600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr14:56168200-56168800	Enhancers	NH-A	brain
37	chr14:56168200-56169000	Enhancers	A549	lung
38	chr14:56168200-56169000	Enhancers	NHDF-Ad	bronchial
39	chr14:56168200-56169000	Enhancers	Osteobl	bone
40	chr14:56168200-56169200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:56168200-56169200	Enhancers	HMEC	breast
42	chr14:56168200-56169600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr14:56168400-56168600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:56168400-56168800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr14:56168400-56168800	Enhancers	Fetal Kidney	kidney
46	chr14:56168400-56168800	Enhancers	HSMM	muscle
47	chr14:56168400-56169000	Enhancers	NHEK	skin
48	chr14:56168400-56169400	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links