Variant report

Variant	rs10889029
Chromosome Location	chr1:57625728-57625729
allele	C/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:18)

rs_ID	r²[population]
rs10789046	0.84[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10889027	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10889028	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889030	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10889031	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11206990	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs155287	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs155288	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs155315	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs155316	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1831870	0.87[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs524370	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs624526	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6680429	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6693209	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539865	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7546422	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9970802	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[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	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	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
3	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
rs10889029	C8A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57621400-57627800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:57622000-57628000	Weak transcription	Pancreas	Pancrea
3	chr1:57623200-57635400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:57623400-57626200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:57623800-57629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:57624000-57644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:57624200-57628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:57624200-57628800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:57624400-57628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:57624400-57629000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:57624600-57628400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:57624800-57626000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:57624800-57627600	Weak transcription	Fetal Brain Female	brain
14	chr1:57624800-57628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:57625600-57625800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:57625600-57625800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:57625600-57626000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr1:57625600-57626400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:57625600-57627000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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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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