Variant report

Variant	rs4894013
Chromosome Location	chr2:179208524-179208525
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	chr2:179206232..179209041-chr2:179210960..179213255,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12151447	0.82[EUR][1000 genomes]
rs12464380	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12464806	0.91[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12467040	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12467053	0.86[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs12471790	0.86[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs12471986	0.84[MEX][hapmap]
rs12473890	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12474919	0.83[EUR][1000 genomes]
rs12478760	0.93[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs12478837	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12479281	0.84[EUR][1000 genomes]
rs13402976	0.85[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1434082	0.82[EUR][1000 genomes]
rs1434083	0.86[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs16866272	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs334603	0.89[MEX][hapmap]
rs334611	0.89[MEX][hapmap]
rs4894008	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4894009	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4894012	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs62176070	0.81[AMR][1000 genomes]
rs62176071	0.82[AMR][1000 genomes]
rs62176072	0.82[AMR][1000 genomes]
rs62176078	0.83[AMR][1000 genomes]
rs6433718	0.84[MEX][hapmap]
rs6718010	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6760059	0.85[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73032523	0.82[AMR][1000 genomes]
rs73032568	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7559125	0.82[AMR][1000 genomes]
rs7559527	0.82[AMR][1000 genomes]
rs7570485	0.82[AMR][1000 genomes]
rs7576065	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7576231	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7587155	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7599195	0.82[AMR][1000 genomes]
rs9646740	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.96[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
rs4894013	HOXD4	cis	cerebellum	SCAN
rs4894013	PVR	trans	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179183800-179247800	Weak transcription	Psoas Muscle	Psoas
2	chr2:179189800-179217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:179193000-179214600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:179193200-179210400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:179193200-179216200	Weak transcription	Adipose Nuclei	Adipose
6	chr2:179193400-179215000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:179194600-179229400	Weak transcription	K562	blood
8	chr2:179195400-179214600	Weak transcription	Left Ventricle	heart
9	chr2:179195400-179229000	Weak transcription	Brain Substantia Nigra	brain
10	chr2:179195600-179214200	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:179195600-179214800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:179196600-179213600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:179197000-179209000	Weak transcription	Esophagus	oesophagus
14	chr2:179198400-179227400	Weak transcription	NHEK	skin
15	chr2:179199000-179241200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:179199200-179214400	Weak transcription	Lung	lung
17	chr2:179199200-179214600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:179199600-179240400	Weak transcription	Fetal Stomach	stomach
19	chr2:179201600-179218400	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:179201800-179214000	Weak transcription	Fetal Brain Female	brain
21	chr2:179201800-179214200	Weak transcription	Brain Angular Gyrus	brain
22	chr2:179201800-179214400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:179201800-179214800	Weak transcription	Brain Germinal Matrix	brain
24	chr2:179201800-179216000	Weak transcription	Right Ventricle	heart
25	chr2:179201800-179216800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:179201800-179217000	Weak transcription	Aorta	Aorta
27	chr2:179201800-179240000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:179201800-179240400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:179201800-179240400	Weak transcription	HSMMtube	muscle
30	chr2:179201800-179253600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:179201800-179268200	Weak transcription	HSMM	muscle
32	chr2:179202000-179216400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:179202400-179214600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:179202400-179215000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:179202400-179216400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:179202400-179216400	Weak transcription	Ovary	ovary
37	chr2:179202400-179227400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:179202400-179230600	Weak transcription	Fetal Brain Male	brain
39	chr2:179202400-179248000	Weak transcription	NH-A	brain
40	chr2:179203600-179213800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:179203800-179213400	Weak transcription	Liver	Liver
42	chr2:179205600-179208800	Weak transcription	HMEC	breast
43	chr2:179205800-179210000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:179206800-179218600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:179207200-179214600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:179207600-179210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:179207800-179217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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