Variant report

Variant	rs12464806
Chromosome Location	chr2:179197251-179197252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12151447	0.84[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12464380	0.91[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12467040	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12467053	0.86[GIH][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12471790	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12473890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12474919	1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12478760	0.92[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs12478837	0.91[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12479281	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13402976	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1434082	0.88[EUR][1000 genomes]
rs1434083	0.86[GIH][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16866272	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4893850	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4894006	0.84[AMR][1000 genomes]
rs4894008	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4894009	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4894012	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4894013	0.91[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62176069	0.86[AMR][1000 genomes]
rs62176070	0.87[AMR][1000 genomes]
rs62176071	0.84[AMR][1000 genomes]
rs62176072	0.84[AMR][1000 genomes]
rs62176076	0.93[AMR][1000 genomes]
rs62176078	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62179162	0.84[AMR][1000 genomes]
rs62179163	0.84[AMR][1000 genomes]
rs62179164	0.84[AMR][1000 genomes]
rs62179167	0.85[AMR][1000 genomes]
rs6718010	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6760059	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73032523	0.84[AMR][1000 genomes]
rs73032568	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7349264	0.92[AMR][1000 genomes]
rs7559125	0.84[AMR][1000 genomes]
rs7559527	0.84[AMR][1000 genomes]
rs7570485	0.84[AMR][1000 genomes]
rs7576065	0.91[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7576231	0.91[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7587155	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7599195	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9646740	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12464806	HOXD4	cis	cerebellum	SCAN
rs12464806	FKBP7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179164600-179200800	Weak transcription	Aorta	Aorta
2	chr2:179176200-179198000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:179183800-179247800	Weak transcription	Psoas Muscle	Psoas
4	chr2:179185400-179198200	Weak transcription	Fetal Lung	lung
5	chr2:179189200-179201200	Weak transcription	Ovary	ovary
6	chr2:179189400-179201200	Weak transcription	Fetal Brain Male	brain
7	chr2:179189800-179217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:179192600-179198600	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:179192600-179200600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:179193000-179201400	Weak transcription	NH-A	brain
11	chr2:179193000-179201800	Weak transcription	Fetal Kidney	kidney
12	chr2:179193000-179214600	Weak transcription	Fetal Intestine Large	intestine
13	chr2:179193200-179199800	Enhancers	HSMMtube	muscle
14	chr2:179193200-179201000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:179193200-179201400	Weak transcription	Fetal Brain Female	brain
16	chr2:179193200-179210400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:179193200-179216200	Weak transcription	Adipose Nuclei	Adipose
18	chr2:179193400-179203400	Weak transcription	Fetal Intestine Small	intestine
19	chr2:179193400-179204800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:179193400-179215000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:179194600-179229400	Weak transcription	K562	blood
22	chr2:179195000-179199200	Enhancers	HSMM	muscle
23	chr2:179195400-179214600	Weak transcription	Left Ventricle	heart
24	chr2:179195400-179229000	Weak transcription	Brain Substantia Nigra	brain
25	chr2:179195600-179214200	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:179195600-179214800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:179195800-179198600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:179196000-179201000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:179196200-179207000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:179196400-179201200	Weak transcription	Brain Germinal Matrix	brain
31	chr2:179196600-179197800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:179196600-179201000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:179196600-179204600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:179196600-179213600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:179196800-179198000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:179197000-179197400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:179197000-179198200	Weak transcription	Liver	Liver
38	chr2:179197000-179198200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:179197000-179198200	Weak transcription	NHEK	skin
40	chr2:179197000-179200000	Weak transcription	HMEC	breast
41	chr2:179197000-179200800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:179197000-179201000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:179197000-179201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:179197000-179209000	Weak transcription	Esophagus	oesophagus
45	chr2:179197200-179198200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:179197200-179198400	Weak transcription	HepG2	liver
47	chr2:179197200-179201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:179197200-179201000	Weak transcription	Gastric	stomach

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