Variant report

Variant	rs2454678
Chromosome Location	chr3:98578096-98578097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1062196	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12107050	0.86[EUR][1000 genomes]
rs12330170	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12490832	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13060012	0.86[EUR][1000 genomes]
rs14310	0.84[ASN][1000 genomes]
rs1440150	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1440151	0.84[EUR][1000 genomes]
rs1440152	0.83[EUR][1000 genomes]
rs17270593	0.85[EUR][1000 genomes]
rs1837500	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1866677	0.88[ASN][1000 genomes]
rs1866678	0.88[ASN][1000 genomes]
rs1866679	0.86[ASN][1000 genomes]
rs1875086	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2028393	0.90[ASN][1000 genomes]
rs2119187	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2119188	0.92[ASN][1000 genomes]
rs2262597	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2279761	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2290067	0.82[ASN][1000 genomes]
rs2334230	0.84[EUR][1000 genomes]
rs2439213	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2439214	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439215	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2439217	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439218	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2439220	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439222	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2439223	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2439225	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2439226	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439228	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2439229	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439231	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2439236	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2454673	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2454676	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2454677	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454680	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454682	0.94[ASN][1000 genomes]
rs2454684	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2454685	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2454691	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2470857	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470859	0.94[ASN][1000 genomes]
rs2470860	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470861	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470864	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470865	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470867	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470869	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2470879	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2470881	0.90[ASN][1000 genomes]
rs2470885	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28802000	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2919236	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2960190	0.86[ASN][1000 genomes]
rs34234373	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34558202	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755576	0.84[EUR][1000 genomes]
rs3772098	0.83[EUR][1000 genomes]
rs3772099	0.84[EUR][1000 genomes]
rs3772101	0.85[EUR][1000 genomes]
rs3772102	0.84[EUR][1000 genomes]
rs3821359	0.83[EUR][1000 genomes]
rs4269027	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4425200	0.82[ASN][1000 genomes]
rs4425201	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4426625	0.82[ASN][1000 genomes]
rs4426626	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4450736	0.82[ASN][1000 genomes]
rs4494869	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62278486	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6782630	0.84[ASN][1000 genomes]
rs6785935	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788418	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788689	0.88[ASN][1000 genomes]
rs6790650	0.82[EUR][1000 genomes]
rs6804850	0.82[ASN][1000 genomes]
rs6808116	0.84[EUR][1000 genomes]
rs704585	0.85[EUR][1000 genomes]
rs7431448	0.84[EUR][1000 genomes]
rs7611929	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7612036	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7612605	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7616275	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7630800	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828609	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs844160	0.83[EUR][1000 genomes]
rs9289683	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9289685	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9811305	0.85[EUR][1000 genomes]
rs9811860	0.88[ASN][1000 genomes]
rs9814819	0.88[ASN][1000 genomes]
rs9820384	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9823430	0.88[ASN][1000 genomes]
rs9845558	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9860216	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9860264	0.89[ASN][1000 genomes]
rs9866570	0.84[EUR][1000 genomes]
rs9867586	0.83[ASN][1000 genomes]
rs9872152	0.84[EUR][1000 genomes]
rs9873932	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878392	0.84[EUR][1000 genomes]
rs9881519	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9883516	0.82[ASN][1000 genomes]
rs9883537	0.82[ASN][1000 genomes]
rs999147	0.82[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	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
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2454678	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98536200-98594200	Weak transcription	HepG2	liver
2	chr3:98537000-98592800	Weak transcription	K562	blood
3	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
4	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:98567400-98578200	Weak transcription	Ovary	ovary
6	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:98572400-98579200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:98573000-98579200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:98574600-98582400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:98574800-98578200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:98575000-98579400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:98575200-98578400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:98575200-98590200	Weak transcription	HSMMtube	muscle
14	chr3:98575400-98578400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
15	chr3:98575400-98579200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:98575400-98583800	Weak transcription	HSMM	muscle
17	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:98575600-98578200	ZNF genes & repeats	Fetal Stomach	stomach
19	chr3:98575600-98579000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:98575600-98583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:98575800-98578200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:98575800-98578800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:98575800-98583600	Weak transcription	NH-A	brain
24	chr3:98575800-98583600	Weak transcription	Osteobl	bone
25	chr3:98575800-98593200	Weak transcription	HUVEC	blood vessel
26	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:98576000-98578200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:98576000-98578200	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr3:98576000-98589800	Weak transcription	HMEC	breast
31	chr3:98576000-98590400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:98576000-98598600	Weak transcription	Fetal Kidney	kidney
33	chr3:98576200-98578200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
34	chr3:98576200-98579000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:98576600-98583000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:98576800-98578200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:98576800-98578400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:98576800-98578800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:98576800-98578800	Weak transcription	Primary T cells from cord blood	blood
40	chr3:98577200-98583200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:98577200-98598800	Weak transcription	Left Ventricle	heart
42	chr3:98577400-98578800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:98577400-98579000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:98578000-98578200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:98578000-98578800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:98578000-98578800	Strong transcription	A549	lung
47	chr3:98578000-98583600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:98578000-98583600	Weak transcription	Dnd41	blood
49	chr3:98578000-98587400	Weak transcription	NHEK	skin
50	chr3:98578000-98588800	Weak transcription	NHLF	lung

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