Variant report

Variant	rs2960190
Chromosome Location	chr3:98589650-98589651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1123293	0.82[EUR][1000 genomes]
rs1837500	0.87[ASN][1000 genomes]
rs1866677	0.80[EUR][1000 genomes]
rs1866678	0.80[EUR][1000 genomes]
rs1866679	0.80[EUR][1000 genomes]
rs1875086	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1967009	0.81[EUR][1000 genomes]
rs2028393	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119187	0.91[ASN][1000 genomes]
rs2119188	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2128051	0.83[EUR][1000 genomes]
rs2128054	0.83[EUR][1000 genomes]
rs2249740	0.81[EUR][1000 genomes]
rs2262597	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439213	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439214	0.85[ASN][1000 genomes]
rs2439215	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439217	0.86[ASN][1000 genomes]
rs2439218	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439220	0.91[ASN][1000 genomes]
rs2439222	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439223	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439225	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439226	0.87[ASN][1000 genomes]
rs2439228	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439229	0.83[ASN][1000 genomes]
rs2439231	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2439236	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449039	0.83[EUR][1000 genomes]
rs2449041	0.83[EUR][1000 genomes]
rs2454673	0.87[ASN][1000 genomes]
rs2454676	0.86[ASN][1000 genomes]
rs2454677	0.87[ASN][1000 genomes]
rs2454678	0.86[ASN][1000 genomes]
rs2454680	0.89[ASN][1000 genomes]
rs2454682	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2454684	0.91[ASN][1000 genomes]
rs2454685	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2454686	0.83[EUR][1000 genomes]
rs2454691	0.86[ASN][1000 genomes]
rs2470857	0.91[ASN][1000 genomes]
rs2470859	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2470860	0.91[ASN][1000 genomes]
rs2470861	0.91[ASN][1000 genomes]
rs2470864	0.86[ASN][1000 genomes]
rs2470865	0.85[ASN][1000 genomes]
rs2470867	0.83[ASN][1000 genomes]
rs2470869	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2470876	0.83[EUR][1000 genomes]
rs2470879	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2470881	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470885	0.86[ASN][1000 genomes]
rs2919236	0.83[ASN][1000 genomes]
rs4450736	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6788689	0.80[EUR][1000 genomes]
rs7630800	0.91[ASN][1000 genomes]
rs9289683	0.87[ASN][1000 genomes]
rs9289685	0.86[ASN][1000 genomes]
rs9811860	0.81[EUR][1000 genomes]
rs9814819	0.80[EUR][1000 genomes]
rs9823430	0.81[EUR][1000 genomes]
rs9860264	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9867586	0.81[EUR][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	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	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
6	esv3441569	chr3:98585311-98607020	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2960190	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 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	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:98575200-98590200	Weak transcription	HSMMtube	muscle
6	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:98575800-98593200	Weak transcription	HUVEC	blood vessel
8	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:98576000-98589800	Weak transcription	HMEC	breast
11	chr3:98576000-98590400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:98576000-98598600	Weak transcription	Fetal Kidney	kidney
13	chr3:98577200-98598800	Weak transcription	Left Ventricle	heart
14	chr3:98578000-98590400	Weak transcription	Adipose Nuclei	Adipose
15	chr3:98578000-98601000	Weak transcription	Lung	lung
16	chr3:98578200-98590400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:98583800-98590800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:98584400-98589800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:98584400-98590000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:98584400-98590000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:98584400-98590200	Weak transcription	NHDF-Ad	bronchial
23	chr3:98584400-98591000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:98584400-98591000	Weak transcription	Dnd41	blood
25	chr3:98584400-98593400	Weak transcription	Fetal Heart	heart
26	chr3:98584400-98607200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:98584600-98604200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:98586200-98591400	Strong transcription	NH-A	brain
29	chr3:98586200-98594000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:98586200-98595800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:98586400-98594000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:98586600-98591200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:98586600-98594200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:98586600-98598600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:98586800-98590600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:98587200-98596200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:98587200-98604600	Weak transcription	Ovary	ovary
38	chr3:98587400-98591000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:98587400-98594200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr3:98587400-98595600	Strong transcription	NHEK	skin
41	chr3:98587800-98601800	Strong transcription	HSMM	muscle
42	chr3:98588000-98590400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:98588200-98591000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:98588800-98590800	Weak transcription	Liver	Liver
45	chr3:98588800-98592400	ZNF genes & repeats	A549	lung
46	chr3:98589000-98592800	Strong transcription	Osteobl	bone
47	chr3:98589000-98594200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:98589000-98598600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:98589200-98591200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:98589200-98602200	Weak transcription	NHLF	lung

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