Variant report

Variant	rs630417
Chromosome Location	chr1:57468023-57468024
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1342435	0.93[ASN][1000 genomes]
rs1411013	0.92[ASN][1000 genomes]
rs1411014	0.92[ASN][1000 genomes]
rs1418473	0.92[ASN][1000 genomes]
rs1418475	0.89[ASN][1000 genomes]
rs17409911	0.93[ASN][1000 genomes]
rs1774888	0.93[ASN][1000 genomes]
rs1774905	0.90[ASN][1000 genomes]
rs1774910	0.92[ASN][1000 genomes]
rs2251154	0.92[ASN][1000 genomes]
rs515493	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs526259	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs661586	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.99[ASN][1000 genomes]
rs689342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs72641113	0.93[ASN][1000 genomes]
rs947655	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs630417	SPRED1	trans	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57457800-57480400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57459000-57474600	Weak transcription	Fetal Brain Female	brain
3	chr1:57460400-57483000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:57463800-57482200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:57464200-57473200	Weak transcription	Fetal Heart	heart
6	chr1:57464600-57468400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:57465400-57470600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:57466800-57473800	Weak transcription	Brain Germinal Matrix	brain
9	chr1:57466800-57474000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:57468000-57469000	Strong transcription	Fetal Intestine Large	intestine
11	chr1:57468000-57470200	Enhancers	Liver	Liver

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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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