Variant report

Variant	rs9812300
Chromosome Location	chr3:23531119-23531120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23526588..23528958-chr3:23530661..23532883,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11914576	0.90[ASN][1000 genomes]
rs11916447	0.82[EUR][1000 genomes]
rs11919065	0.90[ASN][1000 genomes]
rs11921580	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs11926217	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12185989	0.85[JPT][hapmap]
rs12630883	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12633613	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12634459	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12636682	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12637722	0.87[GIH][hapmap]
rs17013412	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17013457	0.88[GIH][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs1826847	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1908772	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2133330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34710747	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4399836	0.89[EUR][1000 genomes]
rs4642064	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55666330	0.93[ASN][1000 genomes]
rs55732421	0.93[ASN][1000 genomes]
rs55934161	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56964757	0.95[ASN][1000 genomes]
rs57172051	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57234542	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57258152	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57278918	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57604595	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57801020	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58068931	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58486254	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59580282	0.90[ASN][1000 genomes]
rs60221455	0.91[ASN][1000 genomes]
rs60759404	0.90[ASN][1000 genomes]
rs6550761	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6763074	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6775891	0.87[GIH][hapmap]
rs6775907	0.88[GIH][hapmap];0.82[TSI][hapmap]
rs6778020	0.92[ASN][1000 genomes]
rs6778478	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6781388	0.92[ASN][1000 genomes]
rs6782079	0.88[GIH][hapmap];0.82[TSI][hapmap]
rs6792462	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs6799118	0.89[ASN][1000 genomes]
rs6799234	0.84[CEU][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs6804201	0.85[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6807390	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6807788	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73043636	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73043687	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73045615	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73045617	0.94[ASN][1000 genomes]
rs73045660	0.90[ASN][1000 genomes]
rs7609845	0.81[GIH][hapmap]
rs7610906	0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7613969	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs7617659	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620266	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7631705	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7632520	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7632814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7635784	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7640458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643270	0.92[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651175	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9835324	0.84[EUR][1000 genomes]
rs9854488	0.89[EUR][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	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9812300	SGOL1	cis	parietal	SCAN
rs9812300	SLC4A7	cis	cerebellum	SCAN
rs9812300	RPL15	cis	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23521000-23531800	Weak transcription	NHDF-Ad	bronchial
2	chr3:23521600-23532000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:23522000-23531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:23523200-23536800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:23523600-23542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:23524000-23534800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:23526000-23532000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:23526600-23554000	Weak transcription	Primary T cells from cord blood	blood
9	chr3:23527800-23533200	Weak transcription	Aorta	Aorta
10	chr3:23528000-23542200	Weak transcription	Right Ventricle	heart
11	chr3:23528400-23531400	Weak transcription	NHLF	lung
12	chr3:23528600-23531400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:23528600-23542200	Weak transcription	Primary B cells from cord blood	blood
14	chr3:23528600-23552200	Weak transcription	Ovary	ovary
15	chr3:23528800-23531200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:23528800-23536600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:23528800-23536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:23529000-23531200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:23529400-23532000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:23529400-23532000	Enhancers	Fetal Heart	heart
21	chr3:23530000-23532800	Enhancers	HUVEC	blood vessel
22	chr3:23530200-23532600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:23530400-23531800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:23530400-23532400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:23530400-23532400	Enhancers	Osteobl	bone
26	chr3:23530600-23542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:23530800-23531200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:23530800-23531400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:23530800-23531400	Enhancers	Right Atrium	heart
30	chr3:23530800-23531600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:23530800-23531600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:23530800-23532000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr3:23530800-23532200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr3:23530800-23532200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr3:23530800-23532200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:23530800-23532400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:23531000-23531200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:23531000-23531200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:23531000-23531200	Enhancers	Psoas Muscle	Psoas
40	chr3:23531000-23531400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:23531000-23531400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:23531000-23531400	Enhancers	Left Ventricle	heart
43	chr3:23531000-23531600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:23531000-23532200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:23531000-23532200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr3:23531000-23532200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:23531000-23532200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:23531000-23532400	Enhancers	NH-A	brain

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