Variant report

Variant	rs9289685
Chromosome Location	chr3:98622653-98622654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:98622620-98622770	HMF	breast:	n/a	n/a
2	POLR2A	chr3:98622564-98622939	HCT-116	colon:	n/a	n/a
3	CTCF	chr3:98622600-98622750	HRPEpiC	eye:	n/a	n/a
4	CTCF	chr3:98622635-98622895	IMR90	lung:	n/a	n/a
5	CTCF	chr3:98622640-98622790	AG04449	skin:	n/a	n/a
6	RAD21	chr3:98622616-98622892	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr3:98622640-98622790	RPTEC	kidney:	n/a	n/a
8	CTCF	chr3:98622640-98622790	AoAF	blood vessel:	n/a	n/a
9	RAD21	chr3:98622558-98622959	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr3:98622561-98622938	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:98622640-98622790	HRE	kidney:	n/a	n/a
12	CTCF	chr3:98622640-98622790	A549	lung:	n/a	n/a
13	CTCF	chr3:98622600-98622750	GM12866	blood:	n/a	n/a
14	CTCF	chr3:98622640-98622790	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr3:98622540-98622866	K562	blood:	n/a	n/a
16	CTCF	chr3:98622640-98622790	AG04450	lung:	n/a	n/a
17	CTCF	chr3:98622531-98622866	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98620298..98622928-chr3:98626076..98627807,2	MCF-7	breast:

No data

Variant related genes	Relation type
DCBLD2	TF binding region
RNU6-1263P	TF binding region
ENSG00000207331	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1062196	0.83[EUR][1000 genomes]
rs1123293	0.87[ASN][1000 genomes]
rs12054181	0.87[ASN][1000 genomes]
rs12107050	0.83[EUR][1000 genomes]
rs12330170	0.83[EUR][1000 genomes]
rs12490832	0.83[EUR][1000 genomes]
rs13060012	0.83[EUR][1000 genomes]
rs1383905	0.87[ASN][1000 genomes]
rs1440150	0.85[EUR][1000 genomes]
rs1440151	0.83[EUR][1000 genomes]
rs1440152	0.82[EUR][1000 genomes]
rs1481634	0.87[ASN][1000 genomes]
rs1481635	0.87[ASN][1000 genomes]
rs1481636	0.87[ASN][1000 genomes]
rs1481637	0.87[ASN][1000 genomes]
rs17270593	0.83[EUR][1000 genomes]
rs1837500	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875086	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1967009	0.87[ASN][1000 genomes]
rs2028393	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2119187	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2119188	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2128051	0.87[ASN][1000 genomes]
rs2128054	0.87[ASN][1000 genomes]
rs2246861	0.87[ASN][1000 genomes]
rs2249740	0.89[ASN][1000 genomes]
rs2262597	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2279761	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2334230	0.83[EUR][1000 genomes]
rs2439213	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439214	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439215	0.90[ASN][1000 genomes]
rs2439217	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439218	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2439220	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439222	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2439223	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2439225	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2439226	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439228	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2439229	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439231	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2439236	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2449001	0.87[ASN][1000 genomes]
rs2449039	0.87[ASN][1000 genomes]
rs2449040	0.87[ASN][1000 genomes]
rs2449041	0.87[ASN][1000 genomes]
rs2449042	0.87[ASN][1000 genomes]
rs2454673	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454676	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2454677	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2454678	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2454680	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454682	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2454684	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2454685	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2454686	0.90[ASN][1000 genomes]
rs2454691	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470821	0.87[ASN][1000 genomes]
rs2470822	0.87[ASN][1000 genomes]
rs2470823	0.87[ASN][1000 genomes]
rs2470824	0.87[ASN][1000 genomes]
rs2470825	0.87[ASN][1000 genomes]
rs2470826	0.87[ASN][1000 genomes]
rs2470845	0.83[ASN][1000 genomes]
rs2470851	0.87[ASN][1000 genomes]
rs2470857	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470859	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2470860	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470861	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470864	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2470865	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470867	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470869	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2470876	0.87[ASN][1000 genomes]
rs2470879	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2470881	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2470885	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608112	0.84[ASN][1000 genomes]
rs28802000	0.86[EUR][1000 genomes]
rs2919236	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2960190	0.86[ASN][1000 genomes]
rs34234373	0.86[EUR][1000 genomes]
rs34558202	0.86[EUR][1000 genomes]
rs3755576	0.83[EUR][1000 genomes]
rs3772098	0.83[EUR][1000 genomes]
rs3772099	0.83[EUR][1000 genomes]
rs3772101	0.83[EUR][1000 genomes]
rs3772102	0.82[EUR][1000 genomes]
rs3821359	0.83[EUR][1000 genomes]
rs4269027	0.81[EUR][1000 genomes]
rs4425201	0.83[EUR][1000 genomes]
rs4426626	0.83[EUR][1000 genomes]
rs4450736	0.92[ASN][1000 genomes]
rs4494869	0.83[EUR][1000 genomes]
rs62276887	0.87[ASN][1000 genomes]
rs62278486	0.83[EUR][1000 genomes]
rs6440280	0.87[ASN][1000 genomes]
rs6785935	0.84[EUR][1000 genomes]
rs6788418	0.85[EUR][1000 genomes]
rs6790650	0.83[EUR][1000 genomes]
rs6793760	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6808116	0.83[EUR][1000 genomes]
rs704585	0.83[EUR][1000 genomes]
rs7431448	0.83[EUR][1000 genomes]
rs7611929	0.83[EUR][1000 genomes]
rs7612036	0.83[EUR][1000 genomes]
rs7612605	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7616275	0.86[EUR][1000 genomes]
rs7630800	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631624	0.87[ASN][1000 genomes]
rs828609	0.83[EUR][1000 genomes]
rs844160	0.82[EUR][1000 genomes]
rs9289683	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9811305	0.83[EUR][1000 genomes]
rs9820384	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9835142	0.87[ASN][1000 genomes]
rs9843864	0.86[ASN][1000 genomes]
rs9845558	0.85[EUR][1000 genomes]
rs9849048	0.82[ASN][1000 genomes]
rs9852950	0.87[ASN][1000 genomes]
rs9860216	0.84[EUR][1000 genomes]
rs9860264	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866570	0.83[EUR][1000 genomes]
rs9872152	0.83[EUR][1000 genomes]
rs9873932	0.85[EUR][1000 genomes]
rs9878392	0.83[EUR][1000 genomes]
rs9881519	0.83[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
rs9289685	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 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	chr3:98621800-98623000	Weak transcription	HUVEC	blood vessel
6	chr3:98621800-98623000	Enhancers	NHDF-Ad	bronchial
7	chr3:98621800-98623200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:98621800-98625000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:98621800-98625000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:98621800-98625000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:98621800-98625000	Weak transcription	Fetal Brain Male	brain
12	chr3:98621800-98625000	Weak transcription	Hela-S3	cervix
13	chr3:98621800-98625000	Weak transcription	HSMMtube	muscle
14	chr3:98622000-98624000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:98622000-98624000	Enhancers	NH-A	brain
16	chr3:98622000-98625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:98622000-98625000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:98622000-98625200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:98622200-98622800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:98622200-98622800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:98622200-98622800	Weak transcription	NHLF	lung
22	chr3:98622200-98623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:98622200-98623200	Weak transcription	Fetal Heart	heart
24	chr3:98622200-98623600	Enhancers	NHEK	skin
25	chr3:98622200-98624000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:98622200-98625000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:98622200-98625000	Weak transcription	Fetal Lung	lung
28	chr3:98622200-98625000	Weak transcription	HMEC	breast
29	chr3:98622200-98625000	Weak transcription	HSMM	muscle
30	chr3:98622200-98625200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:98622400-98622800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:98622400-98622800	Weak transcription	Osteobl	bone
33	chr3:98622600-98622800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:98622600-98622800	Enhancers	GM12878-XiMat	blood
35	chr3:98622600-98623800	Flanking Active TSS	A549	lung

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