Variant report

Variant	rs10789046
Chromosome Location	chr1:57629134-57629135
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10889027	0.81[JPT][hapmap]
rs10889028	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10889029	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]
rs10889030	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10889031	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11206990	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs155287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs155288	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs155315	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs155316	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1831870	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs197109	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs524370	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6680429	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]
rs6693209	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539865	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546422	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9970802	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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
rs10789046	C8A	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57623200-57635400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57624000-57644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57627000-57629400	Enhancers	Fetal Brain Male	brain
4	chr1:57627000-57629800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:57627600-57629600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:57627600-57629600	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:57627600-57629600	Enhancers	Brain Hippocampus Middle	brain
8	chr1:57627800-57629200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:57627800-57629200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:57627800-57629200	Enhancers	Brain Angular Gyrus	brain
11	chr1:57627800-57629200	Enhancers	Brain Germinal Matrix	brain
12	chr1:57627800-57629200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:57627800-57629400	Enhancers	Brain Substantia Nigra	brain
14	chr1:57627800-57629600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:57627800-57629600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:57628000-57629200	Enhancers	Pancreas	Pancrea
17	chr1:57628000-57629800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:57628000-57629800	Enhancers	Brain Anterior Caudate	brain
19	chr1:57628000-57632000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:57628000-57632000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:57628200-57631400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:57628600-57629200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:57628600-57629400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:57628600-57629400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:57628600-57629400	Enhancers	Left Ventricle	heart
26	chr1:57628600-57629600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:57628600-57629600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr1:57628600-57629800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:57628600-57629800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:57628600-57630400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:57628800-57629600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:57628800-57629600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:57629000-57629400	Enhancers	Right Atrium	heart
34	chr1:57629000-57629600	Enhancers	Right Ventricle	heart
35	chr1:57629000-57629800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:57629000-57629800	Enhancers	Lung	lung
37	chr1:57629000-57630000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:57629000-57630000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:57629000-57631200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:57629000-57632000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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