Variant report

Variant	rs9830353
Chromosome Location	chr3:53163953-53163954
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75589741..75590246-chr3:53163554..53164394,2	Hela-S3	cervix:
2	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
3	chr3:53163608..53165597-chr3:53189002..53191742,3	K562	blood:
4	chr3:53163489..53166052-chr3:53379929..53382792,2	K562	blood:
5	chr11:93474325..93475060-chr3:53163950..53164468,2	Hela-S3	cervix:
6	chr14:23564479..23565041-chr3:53163877..53164468,2	Hela-S3	cervix:
7	chr3:53163023..53165298-chr3:53287497..53290275,3	K562	blood:

Variant related genes	Relation type
ENSG00000205084	Chromatin interaction
ENSG00000163931	Chromatin interaction
ENSG00000100813	Chromatin interaction
ENSG00000179933	Chromatin interaction
ENSG00000163932	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000162290	Chromatin interaction
ENSG00000166012	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11130341	0.86[EUR][1000 genomes]
rs12630819	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12638996	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319872	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13433700	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1560332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564929	0.91[ASN][1000 genomes]
rs2564944	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28501212	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734933	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796351	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4282053	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687570	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55950520	0.91[ASN][1000 genomes]
rs56058643	0.91[ASN][1000 genomes]
rs56386026	0.91[ASN][1000 genomes]
rs57261253	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57514626	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61296683	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255925	0.91[ASN][1000 genomes]
rs62255926	0.83[ASN][1000 genomes]
rs62255929	0.91[ASN][1000 genomes]
rs62255931	0.91[ASN][1000 genomes]
rs6445565	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445566	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769931	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769944	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6777975	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783748	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784207	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792345	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792363	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799837	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809973	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73088322	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088327	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088342	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615099	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891369	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9757079	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817467	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820125	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820324	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824325	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828221	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834111	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838517	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844531	0.87[EUR][1000 genomes]
rs9845021	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9845352	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9845484	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858469	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861744	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9867023	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867590	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872260	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878875	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9830353	SERBP1P3	cis	Thyroid	GTEx
rs9830353	RFT1	cis	Esophagus Muscularis	GTEx
rs9830353	RFT1	cis	Artery Tibial	GTEx
rs9830353	RFT1	cis	Artery Aorta	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53162800-53164000	Flanking Active TSS	Dnd41	blood
2	chr3:53163000-53164000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:53163200-53164000	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr3:53163200-53164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:53163200-53164400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr3:53163400-53164000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:53163400-53164000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:53163400-53164000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:53163400-53164000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr3:53163400-53164000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:53163400-53164000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr3:53163400-53164000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:53163400-53164000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:53163400-53164000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:53163400-53164000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:53163400-53164000	Flanking Active TSS	Liver	Liver
17	chr3:53163400-53164000	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr3:53163400-53164000	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr3:53163400-53164000	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr3:53163400-53164000	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr3:53163400-53164000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:53163400-53164000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:53163400-53164000	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr3:53163400-53164000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr3:53163400-53164000	Flanking Active TSS	Fetal Brain Female	brain
26	chr3:53163400-53164000	Flanking Active TSS	Fetal Kidney	kidney
27	chr3:53163400-53164000	Flanking Active TSS	Fetal Lung	lung
28	chr3:53163400-53164000	Flanking Active TSS	Fetal Thymus	thymus
29	chr3:53163400-53164000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr3:53163400-53164000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr3:53163400-53164000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:53163400-53164000	Flanking Active TSS	Stomach Mucosa	stomach
33	chr3:53163400-53164000	Flanking Active TSS	HUVEC	blood vessel
34	chr3:53163400-53164000	Flanking Active TSS	NH-A	brain
35	chr3:53163400-53164000	Flanking Active TSS	NHLF	lung
36	chr3:53163400-53164000	Flanking Active TSS	Osteobl	bone
37	chr3:53163400-53164200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr3:53163400-53164200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr3:53163400-53164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:53163400-53164200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr3:53163400-53164800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:53163400-53165000	Active TSS	Fetal Muscle Trunk	muscle
43	chr3:53163400-53165200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:53163400-53165200	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:53163400-53165200	Active TSS	GM12878-XiMat	blood
46	chr3:53163600-53164000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:53163600-53164000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr3:53163600-53164000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr3:53163600-53164000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr3:53163600-53164000	Flanking Active TSS	Fetal Brain Male	brain

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