Variant report

Variant	rs2359005
Chromosome Location	chr12:51319346-51319347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51319328..51321939-chr12:51438898..51441573,2	K562	blood:
2	chr12:51317560..51319540-chr12:51475708..51478523,2	K562	blood:
3	chr12:51156231..51158960-chr12:51317356..51321250,3	K562	blood:
4	chr12:51316948..51319607-chr12:51419309..51421732,3	K562	blood:
5	chr12:51316948..51319607-chr12:51419309..51421732,2	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10783407	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876108	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs1096033	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1096034	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs11169598	0.80[ASN][1000 genomes]
rs1421435	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2160979	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2243560	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2359006	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2554853	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4638364	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768868	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768931	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4768933	1.00[JPT][hapmap]
rs4768934	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6580774	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs7137881	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7303452	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7311916	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957410	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs7957749	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs829133	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs829140	0.81[EUR][1000 genomes]
rs861204	0.82[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2359005	VDR	cis	cerebellum	SCAN
rs2359005	FKBP11	cis	cerebellum	SCAN
rs2359005	LASS5	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51316600-51321400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr12:51316600-51322000	Active TSS	Aorta	Aorta
3	chr12:51316600-51322000	Active TSS	Right Atrium	heart
4	chr12:51317000-51319600	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr12:51317200-51320800	Active TSS	Psoas Muscle	Psoas
6	chr12:51317400-51319400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:51317600-51319400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr12:51317600-51319400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr12:51317600-51319400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr12:51317600-51319400	Flanking Active TSS	Osteobl	bone
11	chr12:51317600-51320400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr12:51317600-51320800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr12:51317600-51321600	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr12:51317600-51321800	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:51317600-51322800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:51317600-51323200	Active TSS	Brain Substantia Nigra	brain
17	chr12:51317800-51319400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr12:51317800-51319400	Flanking Active TSS	Hela-S3	cervix
19	chr12:51317800-51319400	Flanking Active TSS	NHEK	skin
20	chr12:51317800-51321200	Active TSS	NHDF-Ad	bronchial
21	chr12:51317800-51321400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr12:51317800-51321600	Active TSS	Colonic Mucosa	Colon
23	chr12:51317800-51321600	Active TSS	Left Ventricle	heart
24	chr12:51317800-51322000	Active TSS	Right Ventricle	heart
25	chr12:51317800-51322000	Active TSS	Stomach Smooth Muscle	stomach
26	chr12:51317800-51322400	Active TSS	Brain Anterior Caudate	brain
27	chr12:51317800-51322800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:51317800-51323000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr12:51318000-51319400	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr12:51318000-51319400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr12:51318000-51319400	Flanking Active TSS	Dnd41	blood
32	chr12:51318000-51319600	Flanking Active TSS	HUVEC	blood vessel
33	chr12:51318000-51319800	Flanking Active TSS	Fetal Thymus	thymus
34	chr12:51318000-51320200	Active TSS	Fetal Lung	lung
35	chr12:51318000-51320400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr12:51318000-51320400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:51318000-51320400	Active TSS	Fetal Intestine Large	intestine
38	chr12:51318000-51320400	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr12:51318000-51321200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:51318000-51321200	Active TSS	Thymus	Thymus
41	chr12:51318000-51321600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:51318000-51321600	Active TSS	Brain Hippocampus Middle	brain
43	chr12:51318000-51321800	Active TSS	Lung	lung
44	chr12:51318000-51321800	Active TSS	Pancreas	Pancrea
45	chr12:51318000-51322000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:51318000-51322000	Active TSS	Brain Germinal Matrix	brain
47	chr12:51318000-51322000	Active TSS	Colon Smooth Muscle	Colon
48	chr12:51318000-51322200	Active TSS	Esophagus	oesophagus
49	chr12:51318000-51322200	Active TSS	NHLF	lung
50	chr12:51318000-51322400	Active TSS	Brain Angular Gyrus	brain

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