Variant report

Variant	rs17855824
Chromosome Location	chr3:93779860-93779861
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	chr3:93778962-93779890	K562	blood:	n/a	n/a

Variant related genes	Relation type
NSUN3	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10454213	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070047	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13071953	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13074114	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13092355	0.87[EUR][1000 genomes]
rs13100168	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33944211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34029886	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34333966	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34424617	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34533857	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34703980	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35001908	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35674819	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35772508	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35929728	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35937148	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36049016	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36075561	0.81[ASN][1000 genomes]
rs68145886	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71326806	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73156337	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73156339	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73156384	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156402	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73159590	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73159600	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs73159602	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs73161447	1.00[AFR][1000 genomes]
rs7609644	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615840	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7616142	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7645522	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8178592	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8178615	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8178635	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv967185	chr3:93771419-93794318	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a
14	nsv963340	chr3:93779575-93780186	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93708400-93780800	Weak transcription	K562	blood
2	chr3:93723600-93780800	Weak transcription	Fetal Lung	lung
3	chr3:93723600-93780800	Weak transcription	HSMMtube	muscle
4	chr3:93726200-93780800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:93740600-93780800	Weak transcription	NHDF-Ad	bronchial
6	chr3:93743600-93780800	Weak transcription	Aorta	Aorta
7	chr3:93751000-93780600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:93753800-93780800	Weak transcription	HUVEC	blood vessel
9	chr3:93754200-93781000	Weak transcription	Small Intestine	intestine
10	chr3:93754400-93780800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:93755800-93780800	Weak transcription	Primary B cells from cord blood	blood
12	chr3:93756200-93780600	Weak transcription	GM12878-XiMat	blood
13	chr3:93756200-93780800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:93756200-93780800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:93756200-93780800	Weak transcription	NHEK	skin
16	chr3:93756200-93780800	Weak transcription	Osteobl	bone
17	chr3:93756600-93780800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:93757000-93780800	Weak transcription	HMEC	breast
19	chr3:93761400-93780800	Weak transcription	Brain Anterior Caudate	brain
20	chr3:93762000-93780800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:93762000-93781000	Weak transcription	Psoas Muscle	Psoas
22	chr3:93762600-93780800	Weak transcription	HSMM	muscle
23	chr3:93763600-93780800	Weak transcription	Brain Germinal Matrix	brain
24	chr3:93763600-93780800	Weak transcription	Fetal Brain Female	brain
25	chr3:93763600-93780800	Weak transcription	Right Ventricle	heart
26	chr3:93763600-93781000	Weak transcription	Esophagus	oesophagus
27	chr3:93763600-93781000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:93763600-93781400	Weak transcription	Gastric	stomach
29	chr3:93763800-93780800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:93763800-93780800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:93763800-93780800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:93763800-93780800	Weak transcription	Fetal Intestine Large	intestine
33	chr3:93763800-93781000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:93763800-93781000	Weak transcription	Ovary	ovary
35	chr3:93764000-93780200	Weak transcription	Thymus	Thymus
36	chr3:93764000-93780800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:93764200-93780600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:93764200-93780600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:93764200-93780800	Weak transcription	Adipose Nuclei	Adipose
40	chr3:93764200-93780800	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:93764200-93781000	Weak transcription	Pancreas	Pancrea
42	chr3:93764200-93781400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:93764200-93781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:93764200-93781600	Weak transcription	Spleen	Spleen
45	chr3:93764600-93780200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:93764600-93780800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:93764600-93781000	Weak transcription	Placenta	Placenta
48	chr3:93764800-93780800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:93764800-93780800	Weak transcription	Brain Angular Gyrus	brain
50	chr3:93766200-93780800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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