Variant report

Variant	rs6680429
Chromosome Location	chr1:57637497-57637498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10789046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10889027	0.85[JPT][hapmap]
rs10889028	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10889029	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]
rs10889030	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10889031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155287	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs155288	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs155315	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155316	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831870	0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs197109	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs197110	0.80[JPT][hapmap]
rs524370	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs624526	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6693209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539865	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970802	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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
rs6680429	C8A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57624000-57644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:57632000-57637800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:57633400-57639800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:57636000-57637800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:57636400-57637600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:57636400-57637800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:57636400-57637800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:57636600-57637800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:57636600-57638000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:57636600-57638200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:57636600-57638800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:57636600-57641400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:57636800-57637800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:57637000-57637600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:57637000-57638000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:57637400-57637800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:57637400-57637800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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