Variant report

Variant	rs6852883
Chromosome Location	chr4:141877063-141877064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1001487	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs17424664	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3909595	0.80[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs4956338	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs7666146	0.80[EUR][1000 genomes]
rs7689080	0.80[CEU][hapmap];0.81[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	nsv880167	chr4:141616979-142092124	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830090	chr4:141770494-141947764	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830091	chr4:141796603-141980546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv880168	chr4:141826780-141900370	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6852883	SMARCA5	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:141862200-141891000	Weak transcription	Psoas Muscle	Psoas
2	chr4:141863800-141880600	Weak transcription	Left Ventricle	heart
3	chr4:141864200-141879200	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:141867800-141879000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:141868800-141887400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:141869000-141877200	Weak transcription	Ovary	ovary
7	chr4:141869000-141879400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:141869000-141879600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:141869000-141889000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:141875000-141877200	Enhancers	Colon Smooth Muscle	Colon
11	chr4:141875200-141877600	Enhancers	Fetal Lung	lung
12	chr4:141875600-141877600	Enhancers	Fetal Heart	heart
13	chr4:141875600-141877600	Enhancers	Stomach Smooth Muscle	stomach
14	chr4:141875800-141877600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr4:141876000-141877600	Enhancers	Rectal Smooth Muscle	rectum
16	chr4:141876200-141877600	Enhancers	Fetal Stomach	stomach
17	chr4:141876400-141877200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr4:141876600-141877200	Enhancers	Osteobl	bone
19	chr4:141876600-141877400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:141876600-141877600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:141876600-141877600	Enhancers	Aorta	Aorta
22	chr4:141876800-141877400	Weak transcription	Right Ventricle	heart
23	chr4:141876800-141905600	Weak transcription	Fetal Kidney	kidney
24	chr4:141877000-141890600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:141877000-141892600	Weak transcription	Adipose Nuclei	Adipose

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