Variant report

Variant	rs2470879
Chromosome Location	chr3:98566842-98566843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1062196	0.89[ASN][1000 genomes]
rs1123293	0.85[AMR][1000 genomes]
rs12054181	0.83[AMR][1000 genomes]
rs12107050	0.85[ASN][1000 genomes]
rs12330170	0.87[ASN][1000 genomes]
rs12490832	0.87[ASN][1000 genomes]
rs13060012	0.85[ASN][1000 genomes]
rs1383905	0.83[AMR][1000 genomes]
rs14310	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1440150	0.93[ASN][1000 genomes]
rs1481634	0.83[AMR][1000 genomes]
rs1481635	0.84[AMR][1000 genomes]
rs1481636	0.84[AMR][1000 genomes]
rs1481637	0.84[AMR][1000 genomes]
rs17270593	0.85[ASN][1000 genomes]
rs1837500	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1866677	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866678	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866679	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1875086	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1967009	0.85[AMR][1000 genomes]
rs2028393	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119187	0.91[ASN][1000 genomes]
rs2119188	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2128051	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2128054	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2246861	0.83[AMR][1000 genomes]
rs2249740	0.83[AMR][1000 genomes]
rs2262597	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290067	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439213	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439214	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2439215	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439217	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2439218	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439220	0.91[ASN][1000 genomes]
rs2439222	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439223	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439225	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439226	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2439228	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439229	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2439231	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439236	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2449001	0.84[AMR][1000 genomes]
rs2449039	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2449040	0.84[AMR][1000 genomes]
rs2449041	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2449042	0.85[AMR][1000 genomes]
rs2454673	0.87[ASN][1000 genomes]
rs2454676	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2454677	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2454678	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2454680	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2454682	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2454684	0.91[ASN][1000 genomes]
rs2454685	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2454686	0.80[EUR][1000 genomes]
rs2454691	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2470821	0.83[AMR][1000 genomes]
rs2470822	0.84[AMR][1000 genomes]
rs2470823	0.83[AMR][1000 genomes]
rs2470824	0.84[AMR][1000 genomes]
rs2470825	0.84[AMR][1000 genomes]
rs2470826	0.85[AMR][1000 genomes]
rs2470845	0.82[AMR][1000 genomes]
rs2470857	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2470859	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2470860	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2470861	0.91[ASN][1000 genomes]
rs2470864	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2470865	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2470867	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2470869	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470876	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2470881	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470885	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28608112	0.83[AMR][1000 genomes]
rs28802000	0.93[ASN][1000 genomes]
rs2919236	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2929490	0.80[AMR][1000 genomes]
rs2960190	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34234373	0.93[ASN][1000 genomes]
rs34558202	0.93[ASN][1000 genomes]
rs3755574	0.88[EUR][1000 genomes]
rs3755576	0.82[ASN][1000 genomes]
rs3772101	0.85[ASN][1000 genomes]
rs3772102	0.85[ASN][1000 genomes]
rs4269027	0.85[ASN][1000 genomes]
rs4425200	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4425201	0.87[ASN][1000 genomes]
rs4426625	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4426626	0.87[ASN][1000 genomes]
rs4450736	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4494869	0.87[ASN][1000 genomes]
rs62276887	0.85[AMR][1000 genomes]
rs62278486	0.87[ASN][1000 genomes]
rs6440280	0.83[AMR][1000 genomes]
rs6782630	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6785935	0.93[ASN][1000 genomes]
rs6788418	0.93[ASN][1000 genomes]
rs6788689	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6804850	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808116	0.85[ASN][1000 genomes]
rs704585	0.85[ASN][1000 genomes]
rs7611929	0.87[ASN][1000 genomes]
rs7612036	0.87[ASN][1000 genomes]
rs7612605	0.85[ASN][1000 genomes]
rs7616275	0.93[ASN][1000 genomes]
rs7630800	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs828609	0.87[ASN][1000 genomes]
rs9289683	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9289685	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9811305	0.85[ASN][1000 genomes]
rs9811449	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9811860	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814819	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9815226	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820384	0.81[ASN][1000 genomes]
rs9823430	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835142	0.83[AMR][1000 genomes]
rs9843864	0.85[AMR][1000 genomes]
rs9845558	0.93[ASN][1000 genomes]
rs9852950	0.84[AMR][1000 genomes]
rs9855175	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9860216	0.93[ASN][1000 genomes]
rs9860264	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9867586	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9873932	0.93[ASN][1000 genomes]
rs9878392	0.85[ASN][1000 genomes]
rs9881519	0.92[ASN][1000 genomes]
rs9883516	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9883537	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs999147	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[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
rs2470879	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:98536200-98594200	Weak transcription	HepG2	liver
4	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98537000-98592800	Weak transcription	K562	blood
6	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:98541200-98567000	Weak transcription	Liver	Liver
8	chr3:98550200-98568600	Weak transcription	Thymus	Thymus
9	chr3:98552600-98567000	Weak transcription	Fetal Kidney	kidney
10	chr3:98552800-98575800	Weak transcription	Pancreas	Pancrea
11	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
13	chr3:98553000-98567000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:98553000-98575600	Weak transcription	Fetal Stomach	stomach
15	chr3:98553000-98576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:98553000-98576200	Weak transcription	Left Ventricle	heart
17	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:98558200-98569400	Weak transcription	Fetal Intestine Large	intestine
19	chr3:98558200-98569600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:98558200-98577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:98558400-98568800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:98558800-98567000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:98559000-98567000	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:98559000-98569000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:98559600-98576800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:98559800-98567000	Weak transcription	Dnd41	blood
27	chr3:98559800-98569400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:98560000-98575600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:98560200-98567000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:98560200-98575800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:98561200-98567000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:98561600-98567600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:98562400-98575600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:98563000-98567000	Weak transcription	Fetal Lung	lung
35	chr3:98563000-98574400	Weak transcription	HSMMtube	muscle
36	chr3:98563200-98569000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:98563400-98568800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:98563600-98576000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:98563800-98569200	Strong transcription	NHEK	skin
40	chr3:98564200-98569800	Strong transcription	HMEC	breast
41	chr3:98564600-98567000	Weak transcription	Psoas Muscle	Psoas
42	chr3:98564600-98574800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:98565000-98567800	Strong transcription	HUVEC	blood vessel
44	chr3:98565400-98567000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:98565400-98569600	Weak transcription	Fetal Heart	heart
46	chr3:98565600-98569000	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr3:98565800-98567000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:98565800-98567400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:98565800-98567400	Strong transcription	Ovary	ovary
50	chr3:98566000-98567600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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