Variant report

Variant	rs10020676
Chromosome Location	chr4:173945730-173945731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10019310	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11132976	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721460	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs11722826	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11939508	0.89[EUR][1000 genomes]
rs13125629	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13145272	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17059107	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28451718	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28569824	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3905287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331761	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4557236	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4695821	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832095	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs6833557	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7669563	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680255	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996247	0.86[EUR][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	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10020676	GALNT7	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173941400-173950000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:173942600-173949400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:173942800-173946000	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:173942800-173948800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:173942800-173949400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:173942800-173950000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:173943000-173945800	Weak transcription	Fetal Thymus	thymus
8	chr4:173944600-173946200	Enhancers	Hela-S3	cervix
9	chr4:173944600-173955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:173944800-173945800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:173945000-173945800	Enhancers	Fetal Lung	lung
12	chr4:173945000-173946200	Enhancers	HSMM	muscle
13	chr4:173945400-173946200	Enhancers	HSMMtube	muscle
14	chr4:173945400-173946600	Enhancers	Primary hematopoietic stem cells	blood
15	chr4:173945600-173946000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:173945600-173946200	Weak transcription	A549	lung
17	chr4:173945600-173946800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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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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