Variant report

Variant	rs6466241
Chromosome Location	chr7:78104476-78104477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10241266	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10257012	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10279188	0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10485898	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11763843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12705479	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12705480	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990579	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6466242	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6651114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7791806	0.80[JPT][hapmap]
rs7794954	0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806044	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7808641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9691175	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6466241	CCDC146	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78099800-78106200	Weak transcription	Brain Angular Gyrus	brain
2	chr7:78101800-78105600	Enhancers	Brain Anterior Caudate	brain
3	chr7:78102200-78108200	Weak transcription	Ovary	ovary
4	chr7:78102600-78105000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:78102600-78106400	Weak transcription	HSMMtube	muscle
6	chr7:78103000-78117600	Weak transcription	Fetal Brain Female	brain
7	chr7:78103200-78105000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:78103200-78105800	Weak transcription	HSMM	muscle
9	chr7:78103200-78106000	Weak transcription	Brain Substantia Nigra	brain
10	chr7:78103400-78105400	Weak transcription	Osteobl	bone
11	chr7:78103400-78108600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:78103400-78108600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:78103600-78105400	Enhancers	Fetal Heart	heart
14	chr7:78103800-78115600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:78104200-78104600	Weak transcription	Psoas Muscle	Psoas
16	chr7:78104400-78105600	Enhancers	Brain Hippocampus Middle	brain
17	chr7:78104400-78106600	Enhancers	Brain Cingulate Gyrus	brain
18	chr7:78104400-78116800	Weak transcription	Brain Inferior Temporal Lobe	brain

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

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