Variant report

Variant	rs6860945
Chromosome Location	chr5:16547195-16547196
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	chr5:16482049..16483952-chr5:16545895..16548159,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10035580	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[ASN][1000 genomes]
rs10041159	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs10053746	0.87[CHB][hapmap]
rs10073468	1.00[CEU][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454940	0.83[CHB][hapmap]
rs12187057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12187879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551050	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs17706853	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2028843	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2162770	0.94[ASN][1000 genomes]
rs2560828	0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs56379171	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862083	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs6882868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886993	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[ASN][1000 genomes]
rs7705650	0.98[ASN][1000 genomes]
rs7730689	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9312921	0.98[ASN][1000 genomes]
rs9312922	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6860945	FAM134B	cis	cerebellum	SCAN
rs6860945	FAM134B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16522400-16567400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:16536800-16552800	Weak transcription	Thymus	Thymus
3	chr5:16539200-16554400	Weak transcription	Small Intestine	intestine
4	chr5:16539800-16548400	Weak transcription	Aorta	Aorta
5	chr5:16539800-16548400	Weak transcription	Gastric	stomach
6	chr5:16541200-16548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:16541200-16549600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:16541200-16552000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:16541400-16549800	Weak transcription	HMEC	breast
10	chr5:16542200-16547800	Enhancers	Brain Substantia Nigra	brain
11	chr5:16542600-16567200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:16543200-16547200	Weak transcription	Fetal Intestine Large	intestine
13	chr5:16543200-16548400	Weak transcription	Primary T cells from cord blood	blood
14	chr5:16543200-16548400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:16543400-16547200	Weak transcription	NH-A	brain
17	chr5:16543400-16552800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:16544000-16562400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:16544200-16548800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr5:16544200-16549800	Enhancers	Brain Hippocampus Middle	brain
22	chr5:16544200-16550000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr5:16544200-16565200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:16544400-16549800	Enhancers	Fetal Heart	heart
25	chr5:16544400-16550200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr5:16544600-16549800	Enhancers	Brain Cingulate Gyrus	brain
27	chr5:16544600-16550000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:16545000-16574600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr5:16545200-16549800	Enhancers	Fetal Muscle Leg	muscle
30	chr5:16545600-16548200	Weak transcription	NHDF-Ad	bronchial
31	chr5:16545600-16551600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:16545800-16547600	Enhancers	Pancreas	Pancrea
33	chr5:16546200-16548200	Weak transcription	Right Atrium	heart
34	chr5:16546200-16548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:16546200-16548400	Weak transcription	Psoas Muscle	Psoas
36	chr5:16546200-16552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:16546200-16552800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:16546200-16559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:16546400-16547200	Enhancers	Right Ventricle	heart
40	chr5:16546600-16548400	Weak transcription	Left Ventricle	heart
41	chr5:16546600-16550600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr5:16546800-16549600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:16546800-16550200	Enhancers	Brain Angular Gyrus	brain
44	chr5:16547000-16547200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr5:16547000-16547200	Enhancers	Brain Anterior Caudate	brain
46	chr5:16547000-16547200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr5:16547000-16547200	Flanking Active TSS	Osteobl	bone
48	chr5:16547000-16547400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr5:16547000-16547400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr5:16547000-16547400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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