Variant report

Variant	rs2470828
Chromosome Location	chr3:98702562-98702563
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST3GAL6-2	chr3:98701187-98703298	NONHSAT090834

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs1082398	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082399	1.00[EUR][1000 genomes]
rs1082400	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082402	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082404	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082406	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10935512	1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1383908	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1481633	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1600788	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2133575	0.81[AFR][1000 genomes]
rs2173598	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	1.00[AMR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	1.00[AMR][1000 genomes]
rs2439235	1.00[AMR][1000 genomes]
rs2448985	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes]
rs2454672	1.00[AMR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2454683	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2454690	1.00[AMR][1000 genomes]
rs2470820	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2470839	1.00[AMR][1000 genomes]
rs2470850	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470856	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470858	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470866	1.00[AMR][1000 genomes]
rs2470868	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470874	1.00[AMR][1000 genomes]
rs2470883	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470884	0.81[AFR][1000 genomes]
rs278375	1.00[AMR][1000 genomes]
rs278377	1.00[AMR][1000 genomes]
rs278378	1.00[AMR][1000 genomes]
rs278384	1.00[AMR][1000 genomes]
rs278385	1.00[AMR][1000 genomes]
rs278386	1.00[AMR][1000 genomes]
rs278389	1.00[AMR][1000 genomes]
rs2922213	1.00[AMR][1000 genomes]
rs2929491	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4857107	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5013928	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.84[AFR][1000 genomes]
rs7373983	1.00[AMR][1000 genomes]
rs73858658	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7626395	1.00[AMR][1000 genomes]
rs7630797	1.00[AMR][1000 genomes]
rs774536	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774543	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774546	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774548	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	1.00[AMR][1000 genomes]
rs828606	1.00[AMR][1000 genomes]
rs828607	1.00[AMR][1000 genomes]
rs828619	1.00[AMR][1000 genomes]
rs828620	1.00[AMR][1000 genomes]
rs828622	1.00[AMR][1000 genomes]
rs828623	1.00[AMR][1000 genomes]
rs828624	1.00[AMR][1000 genomes]
rs866873	1.00[AMR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs974982	0.99[AFR][1000 genomes]
rs996199	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98697200-98705000	Weak transcription	HSMMtube	muscle
2	chr3:98699600-98703200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:98699800-98704200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:98700000-98703200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:98700000-98705600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:98700200-98702600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:98700400-98702600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:98700400-98702600	Weak transcription	NHEK	skin
9	chr3:98700400-98703400	Weak transcription	HUVEC	blood vessel
10	chr3:98700400-98704000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:98700800-98704800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:98701000-98705600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:98701200-98703200	Flanking Active TSS	NH-A	brain
14	chr3:98701400-98702800	Enhancers	Brain Germinal Matrix	brain
15	chr3:98701600-98702600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:98701600-98704200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:98701600-98704600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:98701600-98706200	Enhancers	NHDF-Ad	bronchial
19	chr3:98701800-98702800	Strong transcription	HSMM	muscle
20	chr3:98701800-98704000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:98702000-98703200	Transcr. at gene 5' and 3'	HMEC	breast
22	chr3:98702000-98705400	Flanking Active TSS	A549	lung
23	chr3:98702200-98703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:98702200-98703000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:98702200-98704400	Enhancers	NHLF	lung
26	chr3:98702200-98705600	Enhancers	Osteobl	bone
27	chr3:98702400-98702600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:98702400-98703000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:98702400-98703600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:98702400-98705600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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