Variant report

Variant	rs28707457
Chromosome Location	chr3:98459895-98459896
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10470451	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs115931	0.84[ASN][1000 genomes]
rs11923134	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496694	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13315676	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440149	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1440155	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1440158	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1530655	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1868217	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278374	0.88[ASN][1000 genomes]
rs28553326	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755569	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755570	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772091	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821358	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4638909	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56976804	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60464352	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62276459	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62278471	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278472	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611040	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7614161	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620634	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620636	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7628381	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7630887	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7631062	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7643537	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7649812	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7652790	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs828593	0.94[ASN][1000 genomes]
rs828594	0.93[ASN][1000 genomes]
rs828595	0.83[ASN][1000 genomes]
rs828596	0.88[ASN][1000 genomes]
rs828597	0.88[ASN][1000 genomes]
rs828599	0.86[ASN][1000 genomes]
rs828602	0.88[ASN][1000 genomes]
rs828613	0.86[ASN][1000 genomes]
rs844161	0.88[ASN][1000 genomes]
rs893831	0.88[ASN][1000 genomes]
rs893832	0.86[ASN][1000 genomes]
rs9858954	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9859711	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879927	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS 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	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv470783	chr3:98431225-98466222	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28707457	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98453400-98460200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:98453400-98463200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:98453400-98463400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:98453400-98468600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:98453400-98469400	Weak transcription	Aorta	Aorta
6	chr3:98453800-98464200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:98454000-98461800	Weak transcription	Placenta	Placenta
8	chr3:98454000-98464600	Weak transcription	Fetal Brain Male	brain
9	chr3:98454200-98465800	Weak transcription	Fetal Kidney	kidney
10	chr3:98454400-98478000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:98454600-98462000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:98454800-98464200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:98455400-98463000	Weak transcription	Right Atrium	heart
14	chr3:98456000-98462800	Weak transcription	Right Ventricle	heart
15	chr3:98456600-98479600	Weak transcription	Dnd41	blood
16	chr3:98456800-98469800	Weak transcription	Thymus	Thymus
17	chr3:98457400-98463200	Weak transcription	Left Ventricle	heart
18	chr3:98457400-98467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:98457600-98460000	Enhancers	HUVEC	blood vessel
20	chr3:98457800-98460000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:98457800-98474400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:98458000-98461200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:98458200-98461200	Enhancers	Fetal Heart	heart
24	chr3:98458400-98462600	Weak transcription	GM12878-XiMat	blood
25	chr3:98458400-98474800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:98459000-98467200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:98459200-98461400	Enhancers	HepG2	liver
28	chr3:98459200-98462800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:98459400-98460200	Weak transcription	Liver	Liver
30	chr3:98459400-98469400	Weak transcription	Pancreas	Pancrea
31	chr3:98459800-98460000	Enhancers	Fetal Lung	lung
32	chr3:98459800-98460400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:98459800-98460800	Enhancers	A549	lung
34	chr3:98459800-98461000	Enhancers	HMEC	breast
35	chr3:98459800-98461000	Enhancers	NHEK	skin

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