Variant report

Variant	rs4148006
Chromosome Location	chr17:66879417-66879418
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66873136..66876318-chr17:66877176..66880120,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141338	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs6501851	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs73357307	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8068987	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9896422	0.91[CEU][hapmap];0.85[CHB][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv908695	chr17:66865583-66904001	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4148006	SIX4	trans	cerebellum	SCAN
rs4148006	ARSG	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66866800-66883600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr17:66869200-66903400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr17:66869800-66883400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:66873400-66880800	Strong transcription	Fetal Lung	lung
5	chr17:66875400-66881200	Strong transcription	Psoas Muscle	Psoas
6	chr17:66875600-66881400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr17:66876200-66882600	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:66877000-66879800	Strong transcription	Brain Cingulate Gyrus	brain
9	chr17:66877000-66880600	Weak transcription	Right Ventricle	heart
10	chr17:66877000-66881200	Strong transcription	Brain Substantia Nigra	brain
11	chr17:66877000-66881400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:66877000-66882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:66877000-66883800	Strong transcription	Adipose Nuclei	Adipose
14	chr17:66877000-66884000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr17:66877000-66886200	Weak transcription	Colonic Mucosa	Colon
16	chr17:66877000-66886600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr17:66877000-66889000	Weak transcription	Spleen	Spleen
18	chr17:66877000-66906200	Weak transcription	Fetal Stomach	stomach
19	chr17:66877200-66882000	Strong transcription	Left Ventricle	heart
20	chr17:66877200-66882400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr17:66877200-66882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:66877200-66887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr17:66877400-66882600	Weak transcription	Placenta	Placenta
24	chr17:66877600-66881000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:66877600-66888400	Strong transcription	Liver	Liver
26	chr17:66877600-66893400	Weak transcription	Brain Anterior Caudate	brain
27	chr17:66877800-66880000	Strong transcription	Brain Hippocampus Middle	brain
28	chr17:66877800-66880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr17:66877800-66918200	Weak transcription	Fetal Brain Male	brain
30	chr17:66878000-66880000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:66878200-66880800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:66878200-66881800	Strong transcription	Ovary	ovary
33	chr17:66878200-66889400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr17:66878200-66899200	Weak transcription	Osteobl	bone
35	chr17:66878400-66879600	Weak transcription	Fetal Heart	heart
36	chr17:66878400-66901000	Weak transcription	Brain Angular Gyrus	brain
37	chr17:66878600-66880800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:66879200-66879600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
39	chr17:66879400-66879800	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr17:66879400-66879800	Strong transcription	Fetal Muscle Leg	muscle

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