Variant report

Variant	rs10454940
Chromosome Location	chr5:16575395-16575396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10035580	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10041159	0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs10053746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12187057	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12187879	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs1551050	0.83[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs2162770	0.81[ASN][1000 genomes]
rs2560828	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs6860945	0.83[CHB][hapmap]
rs6862083	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs6882868	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs6886993	0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7730689	0.83[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs9312921	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9312922	0.83[CHB][hapmap];0.89[JPT][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	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10454940	FAM134B	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:16549200-16580200	Weak transcription	Gastric	stomach
4	chr5:16566000-16580200	Weak transcription	Right Ventricle	heart
5	chr5:16569200-16580200	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:16571400-16587200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:16571400-16588200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:16571600-16580800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:16572200-16576400	Enhancers	Liver	Liver
10	chr5:16572200-16578800	Weak transcription	Fetal Heart	heart
11	chr5:16572600-16576000	Enhancers	Brain Hippocampus Middle	brain
12	chr5:16572600-16576400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:16572800-16575800	Enhancers	Fetal Brain Male	brain
14	chr5:16572800-16576000	Enhancers	Brain Substantia Nigra	brain
15	chr5:16573200-16576000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:16573400-16576000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:16573400-16576000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:16573400-16576000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:16573400-16576400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr5:16573600-16575400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr5:16573600-16576000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:16573600-16576000	Enhancers	Brain Anterior Caudate	brain
23	chr5:16573600-16576200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr5:16573600-16581200	Weak transcription	Fetal Kidney	kidney
25	chr5:16573800-16585200	Weak transcription	Pancreas	Pancrea
26	chr5:16574000-16575800	Enhancers	Stomach Mucosa	stomach
27	chr5:16574200-16575600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:16574200-16575600	Enhancers	Primary T cells from cord blood	blood
29	chr5:16574200-16575600	Enhancers	Left Ventricle	heart
30	chr5:16574200-16575800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr5:16574200-16575800	Enhancers	Psoas Muscle	Psoas
32	chr5:16574200-16575800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr5:16574200-16576000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr5:16574200-16576000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr5:16574200-16576000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr5:16574200-16576000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:16574200-16576000	Enhancers	Brain Cingulate Gyrus	brain
38	chr5:16574200-16576200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr5:16574200-16576400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr5:16574200-16585200	Weak transcription	Fetal Intestine Small	intestine
41	chr5:16574400-16575400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr5:16574400-16575800	Enhancers	Adipose Nuclei	Adipose
43	chr5:16574400-16575800	Enhancers	Fetal Brain Female	brain
44	chr5:16574400-16576000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:16574400-16576000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:16574400-16576000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:16574400-16576000	Enhancers	Brain Angular Gyrus	brain
48	chr5:16574400-16576000	Enhancers	Brain Germinal Matrix	brain
49	chr5:16574400-16576000	Enhancers	HMEC	breast
50	chr5:16574400-16576000	Enhancers	NHEK	skin

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