Variant report

Variant	rs9860264
Chromosome Location	chr3:98624515-98624516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98620185..98622258-chr3:98623304..98625603,3	MCF-7	breast:
2	chr3:98609933..98612061-chr3:98623742..98626335,2	K562	blood:
3	chr3:98619082..98623514-chr3:98623819..98627236,6	K562	blood:

Variant related genes	Relation type
ENSG00000239462	Chromatin interaction
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1123293	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12054181	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1383905	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs14310	0.81[EUR][1000 genomes]
rs1481634	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1481635	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1481636	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1481637	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1837500	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1866677	0.82[EUR][1000 genomes]
rs1866678	0.82[EUR][1000 genomes]
rs1866679	0.82[EUR][1000 genomes]
rs1875086	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1967009	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2028393	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119187	0.94[ASN][1000 genomes]
rs2119188	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2128051	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2128054	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2246861	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2249740	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2262597	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290067	0.81[EUR][1000 genomes]
rs2439213	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439214	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2439215	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439217	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439218	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439220	0.94[ASN][1000 genomes]
rs2439222	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439223	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439225	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439226	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2439228	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439229	0.86[ASN][1000 genomes]
rs2439231	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439236	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2449001	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449039	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449040	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449041	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449042	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2454673	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2454676	0.89[ASN][1000 genomes]
rs2454677	0.90[ASN][1000 genomes]
rs2454678	0.89[ASN][1000 genomes]
rs2454680	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2454682	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2454684	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2454685	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2454686	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2454691	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2470821	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470822	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470823	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470824	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470825	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470826	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470845	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2470851	0.87[ASN][1000 genomes]
rs2470857	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2470859	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470860	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2470861	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2470864	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2470865	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2470867	0.86[ASN][1000 genomes]
rs2470869	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470876	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470879	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470881	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2470885	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28608112	0.84[ASN][1000 genomes]
rs2919236	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2929490	0.82[EUR][1000 genomes]
rs2960190	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4425200	0.81[EUR][1000 genomes]
rs4426625	0.81[EUR][1000 genomes]
rs4450736	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62276887	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6440280	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782630	0.81[EUR][1000 genomes]
rs6788689	0.82[EUR][1000 genomes]
rs6804850	0.81[EUR][1000 genomes]
rs7630800	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7631624	0.87[ASN][1000 genomes]
rs9289683	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9289685	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9811449	0.81[EUR][1000 genomes]
rs9811860	0.83[EUR][1000 genomes]
rs9814819	0.82[EUR][1000 genomes]
rs9815226	0.81[EUR][1000 genomes]
rs9820384	0.80[ASN][1000 genomes]
rs9823430	0.83[EUR][1000 genomes]
rs9835142	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9843864	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9849048	0.82[ASN][1000 genomes]
rs9852950	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867586	0.83[EUR][1000 genomes]
rs9883516	0.80[EUR][1000 genomes]
rs9883537	0.80[EUR][1000 genomes]
rs999147	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9860264	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98621400-98625000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:98621600-98625000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr3:98621600-98625200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:98621600-98625400	Weak transcription	Psoas Muscle	Psoas
5	chr3:98621800-98625000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:98621800-98625000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:98621800-98625000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:98621800-98625000	Weak transcription	Fetal Brain Male	brain
9	chr3:98621800-98625000	Weak transcription	Hela-S3	cervix
10	chr3:98621800-98625000	Weak transcription	HSMMtube	muscle
11	chr3:98622000-98625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:98622000-98625000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:98622000-98625200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:98622200-98625000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:98622200-98625000	Weak transcription	Fetal Lung	lung
16	chr3:98622200-98625000	Weak transcription	HMEC	breast
17	chr3:98622200-98625000	Weak transcription	HSMM	muscle
18	chr3:98622200-98625200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:98623000-98628000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:98623200-98625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:98623400-98625000	Weak transcription	Osteobl	bone
22	chr3:98623600-98625000	Weak transcription	NHEK	skin
23	chr3:98623600-98636400	Weak transcription	Fetal Heart	heart
24	chr3:98623800-98624800	Weak transcription	HUVEC	blood vessel
25	chr3:98623800-98625000	Enhancers	A549	lung
26	chr3:98624000-98625000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:98624000-98625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:98624000-98625000	Weak transcription	NH-A	brain
29	chr3:98624000-98625000	Weak transcription	NHDF-Ad	bronchial
30	chr3:98624200-98624600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:98624200-98625000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:98624400-98624800	Weak transcription	NHLF	lung

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