Variant report

Variant	rs17816553
Chromosome Location	chr4:7464995-7464996
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10031766	0.82[ASN][1000 genomes]
rs34842798	0.82[ASN][1000 genomes]
rs4303979	0.82[ASN][1000 genomes]
rs4393998	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4420980	0.82[ASN][1000 genomes]
rs4423874	0.82[ASN][1000 genomes]
rs4423875	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4495038	0.82[GIH][hapmap]
rs4525976	0.82[ASN][1000 genomes]
rs4599414	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4689125	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689753	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689754	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4689755	0.84[CEU][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61072122	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61563031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62277623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62277625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62277628	0.89[ASN][1000 genomes]
rs6846363	0.82[ASN][1000 genomes]
rs749994	0.89[ASN][1000 genomes]
rs7653894	0.82[ASN][1000 genomes]
rs7654086	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7675528	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7677309	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7698267	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17816553	CNO	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr4:7462000-7465400	Enhancers	Brain Substantia Nigra	brain
4	chr4:7462000-7465600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:7462200-7465800	Enhancers	Brain Cingulate Gyrus	brain
6	chr4:7462200-7466000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr4:7462400-7465000	Enhancers	Brain Angular Gyrus	brain
8	chr4:7462400-7466000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:7463200-7465000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:7463200-7466000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:7463400-7465000	Enhancers	Fetal Brain Female	brain
12	chr4:7463400-7465600	Enhancers	Brain Anterior Caudate	brain
13	chr4:7463400-7466000	Enhancers	Brain Hippocampus Middle	brain
14	chr4:7463800-7465000	Enhancers	Stomach Mucosa	stomach
15	chr4:7463800-7465600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:7463800-7466000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:7463800-7467400	Enhancers	Brain Germinal Matrix	brain
18	chr4:7464000-7465000	Enhancers	Liver	Liver
19	chr4:7464000-7465000	Enhancers	Fetal Brain Male	brain
20	chr4:7464000-7465800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr4:7464200-7465600	Enhancers	Left Ventricle	heart
22	chr4:7464200-7466600	Enhancers	Fetal Stomach	stomach
23	chr4:7464400-7465000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:7464400-7465400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:7464600-7465800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:7464600-7466000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:7464800-7465000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr4:7464800-7465800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:7464800-7466000	Enhancers	Fetal Muscle Leg	muscle

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