Variant report

Variant	rs2439214
Chromosome Location	chr3:98576367-98576368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1062196	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12107050	0.89[EUR][1000 genomes]
rs12330170	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12490832	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13060012	0.89[EUR][1000 genomes]
rs14310	0.83[ASN][1000 genomes]
rs1440150	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1440151	0.87[EUR][1000 genomes]
rs1440152	0.86[EUR][1000 genomes]
rs17270593	0.88[EUR][1000 genomes]
rs1837500	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1866677	0.87[ASN][1000 genomes]
rs1866678	0.87[ASN][1000 genomes]
rs1866679	0.85[ASN][1000 genomes]
rs1875086	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2028393	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2119187	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2119188	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2262597	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2279761	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2290067	0.81[ASN][1000 genomes]
rs2334230	0.87[EUR][1000 genomes]
rs2439213	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2439215	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2439217	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439218	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2439220	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439222	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439223	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439225	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439226	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439228	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2439229	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439231	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2439236	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2454673	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2454676	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454677	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2454678	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454680	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2454682	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2454684	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2454685	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2454691	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470857	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2470859	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2470860	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2470861	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2470864	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2470865	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470867	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2470869	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2470879	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2470881	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2470885	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28802000	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2919236	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2960190	0.85[ASN][1000 genomes]
rs34234373	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34558202	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3755576	0.87[EUR][1000 genomes]
rs3772098	0.87[EUR][1000 genomes]
rs3772099	0.87[EUR][1000 genomes]
rs3772101	0.88[EUR][1000 genomes]
rs3772102	0.87[EUR][1000 genomes]
rs3821359	0.87[EUR][1000 genomes]
rs4269027	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4425200	0.81[ASN][1000 genomes]
rs4425201	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4426625	0.81[ASN][1000 genomes]
rs4426626	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4450736	0.81[ASN][1000 genomes]
rs4494869	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62278486	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782630	0.83[ASN][1000 genomes]
rs6785935	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6788418	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6788689	0.87[ASN][1000 genomes]
rs6790650	0.86[EUR][1000 genomes]
rs6793760	0.80[EUR][1000 genomes]
rs6804850	0.81[ASN][1000 genomes]
rs6808116	0.87[EUR][1000 genomes]
rs704585	0.88[EUR][1000 genomes]
rs7431448	0.87[EUR][1000 genomes]
rs7611929	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7612036	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7612605	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7616275	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630800	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828609	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs844160	0.86[EUR][1000 genomes]
rs9289683	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9289685	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9811305	0.88[EUR][1000 genomes]
rs9811860	0.87[ASN][1000 genomes]
rs9814819	0.87[ASN][1000 genomes]
rs9820384	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9823430	0.87[ASN][1000 genomes]
rs9845558	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9860216	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9860264	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9866570	0.87[EUR][1000 genomes]
rs9867586	0.82[ASN][1000 genomes]
rs9872152	0.87[EUR][1000 genomes]
rs9873932	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9878392	0.87[EUR][1000 genomes]
rs9881519	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9883516	0.81[ASN][1000 genomes]
rs9883537	0.81[ASN][1000 genomes]
rs999147	0.81[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
rs2439214	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98536200-98594200	Weak transcription	HepG2	liver
3	chr3:98537000-98592800	Weak transcription	K562	blood
4	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
6	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:98558200-98577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:98559600-98576800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:98567400-98578200	Weak transcription	Ovary	ovary
10	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:98567800-98577000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:98568200-98578000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:98568400-98577200	Weak transcription	Dnd41	blood
14	chr3:98572400-98579200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:98573000-98579200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:98574600-98582400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:98574800-98578200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:98575000-98576600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:98575000-98576800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:98575000-98577800	Strong transcription	Fetal Lung	lung
21	chr3:98575000-98579400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:98575200-98576600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:98575200-98576600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:98575200-98577600	Weak transcription	NHLF	lung
25	chr3:98575200-98578000	ZNF genes & repeats	Brain Germinal Matrix	brain
26	chr3:98575200-98578000	ZNF genes & repeats	A549	lung
27	chr3:98575200-98578400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:98575200-98590200	Weak transcription	HSMMtube	muscle
29	chr3:98575400-98577000	ZNF genes & repeats	Liver	Liver
30	chr3:98575400-98578000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr3:98575400-98578400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
32	chr3:98575400-98579200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:98575400-98583800	Weak transcription	HSMM	muscle
34	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:98575600-98576600	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr3:98575600-98577200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr3:98575600-98577400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr3:98575600-98577400	Weak transcription	NHEK	skin
39	chr3:98575600-98578200	ZNF genes & repeats	Fetal Stomach	stomach
40	chr3:98575600-98579000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:98575600-98583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:98575800-98576400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr3:98575800-98576800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:98575800-98576800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:98575800-98578000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:98575800-98578000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:98575800-98578000	ZNF genes & repeats	Fetal Muscle Leg	muscle
48	chr3:98575800-98578200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:98575800-98578800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:98575800-98583600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links