Variant report

Variant	rs12644098
Chromosome Location	chr4:10745417-10745418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10002150	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10007887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516209	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10516211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805246	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10805247	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10938948	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11938512	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11946994	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12643478	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12648342	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16872866	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16872935	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28532032	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729671	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4073342	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4368597	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4420973	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4441748	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4470616	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4485814	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4629442	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6817400	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6828448	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6831297	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6846210	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6848219	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73105702	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7658643	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7676338	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7681266	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7683803	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9291448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291449	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9884398	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
2	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
3	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
4	nsv517971	chr4:10399068-10893253	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv878694	chr4:10407572-10783606	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv878697	chr4:10501373-10831866	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv829860	chr4:10598743-10764854	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv822488	chr4:10709164-10784711	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1004951	chr4:10723763-10771088	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1000613	chr4:10723763-11716982	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	nsv1004121	chr4:10738618-11057063	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv878699	chr4:10744931-10874933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12644098	HS3ST1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10726000-10747800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:10742200-10745800	Enhancers	Primary B cells from peripheral blood	blood
3	chr4:10743000-10746800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:10743000-10747800	Weak transcription	NH-A	brain
5	chr4:10743400-10745800	Flanking Active TSS	GM12878-XiMat	blood
6	chr4:10743600-10747600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:10743600-10747800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:10743600-10752600	Weak transcription	Osteobl	bone
9	chr4:10745200-10746200	Enhancers	Primary B cells from cord blood	blood

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