Variant report

Variant	rs7172656
Chromosome Location	chr15:74056225-74056226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1038093	0.81[JPT][hapmap]
rs12440563	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17187183	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2123208	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28485305	0.84[AMR][1000 genomes]
rs28581503	0.83[AMR][1000 genomes]
rs28688071	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743098	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4243087	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4887161	0.92[ASN][1000 genomes]
rs4887164	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs60833441	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7162423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7171779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471252	chr15:74006691-74089793	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv569970	chr15:74016622-74059081	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7172656	THAP10	cis	cerebellum	SCAN
rs7172656	SCAMP2	cis	parietal	SCAN
rs7172656	COMMD4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74049800-74057000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:74052600-74059000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:74053000-74067000	Weak transcription	Fetal Brain Male	brain
4	chr15:74054400-74057400	Enhancers	Fetal Lung	lung
5	chr15:74055600-74058200	Enhancers	Ovary	ovary
6	chr15:74056000-74057000	Enhancers	Brain Substantia Nigra	brain
7	chr15:74056000-74057200	Enhancers	Brain Angular Gyrus	brain
8	chr15:74056000-74057200	Enhancers	Brain Cingulate Gyrus	brain
9	chr15:74056000-74057400	Enhancers	Fetal Stomach	stomach
10	chr15:74056200-74056800	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr15:74056200-74056800	Bivalent Enhancer	HepG2	liver
12	chr15:74056200-74057000	Enhancers	Left Ventricle	heart
13	chr15:74056200-74057200	Enhancers	Brain Anterior Caudate	brain
14	chr15:74056200-74057200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr15:74056200-74057200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:74056200-74057200	Enhancers	Esophagus	oesophagus
17	chr15:74056200-74057200	Enhancers	Right Atrium	heart
18	chr15:74056200-74057400	Enhancers	Right Ventricle	heart
19	chr15:74056200-74057400	Enhancers	Spleen	Spleen

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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