Variant report

Variant	rs4283935
Chromosome Location	chr7:39311211-39311212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12531819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12701709	0.82[JPT][hapmap]
rs4318977	0.83[JPT][hapmap]
rs4469355	0.83[LWK][hapmap]
rs4629764	0.82[JPT][hapmap]
rs4723836	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs4723837	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723839	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55928878	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67835487	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68122495	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6968851	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][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	nsv1015572	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv538821	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv887969	chr7:39265429-39391875	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4283935	SEPT7	cis	cerebellum	SCAN
rs4283935	CDK13	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39306200-39311800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr7:39310200-39312000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:39310600-39311400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:39310600-39312200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr7:39310800-39311400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr7:39310800-39311400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:39310800-39311400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr7:39310800-39311400	Enhancers	Fetal Brain Female	brain
9	chr7:39310800-39312000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr7:39310800-39312200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:39310800-39312200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr7:39311000-39311400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:39311000-39311400	Enhancers	Fetal Muscle Leg	muscle
14	chr7:39311000-39311400	Active TSS	Stomach Smooth Muscle	stomach
15	chr7:39311000-39311400	Enhancers	HSMMtube	muscle
16	chr7:39311000-39312000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr7:39311000-39312000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr7:39311000-39312000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:39311000-39312000	Enhancers	Fetal Muscle Trunk	muscle
20	chr7:39311000-39312200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:39311200-39311400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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