Variant report

Variant	rs1866679
Chromosome Location	chr3:98518806-98518807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:98516179-98518840	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
3	POLR2A	chr3:98517264-98518824	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr3:98518150-98518901	HCT-116	colon:	n/a	n/a
5	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
6	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1062196	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12107050	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12330170	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12490832	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13060012	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs14310	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440150	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17270593	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1866677	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1866678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1875086	0.83[EUR][1000 genomes]
rs2028393	0.85[EUR][1000 genomes]
rs2119187	0.83[ASN][1000 genomes]
rs2119188	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2262597	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2290067	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439213	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439214	0.85[ASN][1000 genomes]
rs2439215	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439217	0.86[ASN][1000 genomes]
rs2439218	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439220	0.83[ASN][1000 genomes]
rs2439222	0.83[EUR][1000 genomes]
rs2439223	0.83[EUR][1000 genomes]
rs2439225	0.84[EUR][1000 genomes]
rs2439228	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439229	0.91[ASN][1000 genomes]
rs2439231	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2439236	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2454676	0.86[ASN][1000 genomes]
rs2454677	0.87[ASN][1000 genomes]
rs2454678	0.86[ASN][1000 genomes]
rs2454680	0.81[ASN][1000 genomes]
rs2454682	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454684	0.83[ASN][1000 genomes]
rs2454685	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2470857	0.83[ASN][1000 genomes]
rs2470859	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2470860	0.83[ASN][1000 genomes]
rs2470861	0.83[ASN][1000 genomes]
rs2470864	0.86[ASN][1000 genomes]
rs2470865	0.85[ASN][1000 genomes]
rs2470867	0.91[ASN][1000 genomes]
rs2470869	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2470879	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2470881	0.85[EUR][1000 genomes]
rs28802000	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2919236	0.91[ASN][1000 genomes]
rs2960190	0.80[EUR][1000 genomes]
rs34234373	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34558202	0.98[ASN][1000 genomes]
rs3755574	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755576	0.90[ASN][1000 genomes]
rs3772101	0.93[ASN][1000 genomes]
rs3772102	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4425200	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4425201	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4426625	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4426626	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4494869	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62278486	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6782630	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785935	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6788418	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6788689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6790650	0.85[ASN][1000 genomes]
rs6804850	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808116	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs704585	0.93[ASN][1000 genomes]
rs7611929	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7612036	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7616275	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7630800	0.83[ASN][1000 genomes]
rs828609	0.96[ASN][1000 genomes]
rs9811305	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9811449	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9811860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815226	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9823430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9845558	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9855175	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860216	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9860264	0.82[EUR][1000 genomes]
rs9867586	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873932	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9878392	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9881519	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9883516	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883537	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs999147	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs1866679	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
4	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
5	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:98503400-98576400	Weak transcription	Gastric	stomach
8	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:98504600-98519400	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
11	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
13	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
14	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
15	chr3:98506400-98519400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:98506400-98524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:98506800-98523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:98508000-98519600	Weak transcription	Fetal Lung	lung
20	chr3:98508000-98524600	Weak transcription	GM12878-XiMat	blood
21	chr3:98508200-98524600	Weak transcription	Fetal Heart	heart
22	chr3:98512200-98521000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:98512400-98520800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr3:98512800-98520400	Strong transcription	HSMM	muscle
25	chr3:98513000-98520800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:98513000-98524400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:98513400-98520600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:98513400-98520800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:98513400-98520800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:98513400-98523800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:98513600-98520800	Strong transcription	NH-A	brain
32	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
34	chr3:98513800-98520600	Strong transcription	A549	lung
35	chr3:98513800-98520800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:98513800-98520800	Strong transcription	Osteobl	bone
37	chr3:98513800-98521000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:98513800-98524400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:98513800-98525400	Weak transcription	Esophagus	oesophagus
40	chr3:98513800-98526000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:98514000-98519000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:98514000-98520000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:98514000-98520600	Strong transcription	NHDF-Ad	bronchial
44	chr3:98515000-98520200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:98515000-98520400	Strong transcription	HUVEC	blood vessel
46	chr3:98515000-98520600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:98515000-98520600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:98515000-98520800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:98515200-98519400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:98515200-98520600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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