Variant report

Variant	rs12677471
Chromosome Location	chr8:104125084-104125085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10955307	0.82[EUR][1000 genomes]
rs13275878	0.86[EUR][1000 genomes]
rs16870122	0.89[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs16870125	0.89[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][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	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12677471	NCALD	cis	cerebellum	SCAN
rs12677471	SPAG1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104119000-104127800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr8:104119400-104134000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:104121800-104127800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr8:104122000-104126000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr8:104122000-104134600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:104122400-104127000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:104122400-104131200	Weak transcription	NH-A	brain
8	chr8:104122600-104126200	Weak transcription	HSMMtube	muscle
9	chr8:104123200-104126400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:104123200-104126600	Weak transcription	Osteobl	bone
11	chr8:104123400-104127800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr8:104123600-104132600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:104123800-104126400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:104123800-104128200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr8:104124000-104126000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr8:104124200-104127600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr8:104124200-104127800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr8:104124800-104126200	Weak transcription	Gastric	stomach

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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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