Variant report

Variant	rs7675528
Chromosome Location	chr4:7463765-7463766
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10031766	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816553	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs34842798	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234812	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4303979	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380522	0.84[CHD][hapmap]
rs4393998	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420980	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423874	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423875	0.82[ASN][1000 genomes]
rs4525976	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599414	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4689125	0.82[ASN][1000 genomes]
rs4689753	0.82[ASN][1000 genomes]
rs4689754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689755	0.82[ASN][1000 genomes]
rs61072122	0.82[ASN][1000 genomes]
rs61563031	0.82[ASN][1000 genomes]
rs62277623	0.82[ASN][1000 genomes]
rs62277625	0.82[ASN][1000 genomes]
rs6842366	0.86[GIH][hapmap];0.82[JPT][hapmap]
rs6846363	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653894	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698267	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv593569	chr4:7291363-7626136	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1011547	chr4:7318232-7637410	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537017	chr4:7318232-7637410	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv469758	chr4:7370083-7546250	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv878560	chr4:7402284-7475114	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv878561	chr4:7402284-7544610	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
8	nsv878563	chr4:7420785-7529367	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv878564	chr4:7421007-7535214	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
10	nsv878566	chr4:7456717-7529367	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
11	nsv878567	chr4:7456717-7544610	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7675528	ACOX3	cis	cerebellum	SCAN
rs7675528	LOC348926	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7460800-7466000	Enhancers	Ovary	ovary
2	chr4:7461000-7466000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr4:7462000-7464800	Enhancers	Stomach Smooth Muscle	stomach
4	chr4:7462000-7465400	Enhancers	Brain Substantia Nigra	brain
5	chr4:7462000-7465600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:7462200-7464000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr4:7462200-7464400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:7462200-7464800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:7462200-7464800	Enhancers	Fetal Intestine Small	intestine
10	chr4:7462200-7465800	Enhancers	Brain Cingulate Gyrus	brain
11	chr4:7462200-7466000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr4:7462400-7464200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr4:7462400-7465000	Enhancers	Brain Angular Gyrus	brain
14	chr4:7462400-7466000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:7462600-7463800	Enhancers	H9 Cell Line	embryonic stem cell
16	chr4:7462600-7463800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:7462600-7464000	Weak transcription	Liver	Liver
18	chr4:7462600-7464600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr4:7463000-7464800	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr4:7463000-7464800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
21	chr4:7463200-7464400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:7463200-7464600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:7463200-7464800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr4:7463200-7464800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:7463200-7465000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:7463200-7466000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:7463400-7463800	Weak transcription	Brain Germinal Matrix	brain
28	chr4:7463400-7465000	Enhancers	Fetal Brain Female	brain
29	chr4:7463400-7465600	Enhancers	Brain Anterior Caudate	brain
30	chr4:7463400-7466000	Enhancers	Brain Hippocampus Middle	brain
31	chr4:7463600-7463800	Bivalent Enhancer	Stomach Mucosa	stomach
32	chr4:7463600-7464000	Weak transcription	Fetal Brain Male	brain

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