Variant report

Variant	rs388483
Chromosome Location	chr3:50615539-50615540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50614605..50616969-chr3:50624972..50627366,3	K562	blood:
2	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
3	chr3:50614914..50616953-chr3:50617610..50620432,2	MCF-7	breast:
4	chr3:50614741..50617207-chr3:50631389..50633119,2	MCF-7	breast:
5	chr3:50608156..50612219-chr3:50612794..50616407,4	K562	blood:
6	chr3:50613912..50618382-chr3:50647156..50650083,6	K562	blood:
7	chr3:50611626..50614563-chr3:50615388..50617082,2	MCF-7	breast:
8	chr3:50606526..50611586-chr3:50612274..50616724,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000114737	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1034405	0.83[YRI][hapmap]
rs129310	0.85[YRI][hapmap]
rs1385025	0.86[YRI][hapmap]
rs2269505	0.93[YRI][hapmap]
rs2355323	0.93[YRI][hapmap]
rs375544	0.90[YRI][hapmap]
rs3792325	0.90[YRI][hapmap]
rs3792328	0.90[YRI][hapmap]
rs3804627	0.93[YRI][hapmap]
rs396302	0.86[YRI][hapmap]
rs4261877	0.88[AFR][1000 genomes]
rs441516	0.93[YRI][hapmap]
rs443436	0.86[YRI][hapmap]
rs448028	0.86[YRI][hapmap]
rs453570	0.93[YRI][hapmap]
rs4688714	0.84[ASN][1000 genomes]
rs616589	0.90[YRI][hapmap]
rs6446212	0.90[YRI][hapmap]
rs728901	0.89[YRI][hapmap]
rs7646236	0.90[YRI][hapmap]
rs809454	0.93[YRI][hapmap]
rs813243	0.86[YRI][hapmap]
rs900735	0.86[YRI][hapmap]
rs9682401	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs388483	NICN1	cis	cerebellum	SCAN
rs388483	DOCK3	cis	Thyroid	GTEx
rs388483	CACNA2D2	cis	parietal	SCAN
rs388483	TMIE	cis	parietal	SCAN
rs388483	TUSC2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50615600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
3	chr3:50607600-50617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:50607800-50620000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
7	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:50608000-50618400	Weak transcription	NH-A	brain
9	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
11	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:50608200-50616200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:50608200-50617400	Weak transcription	Fetal Brain Male	brain
14	chr3:50608200-50624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:50608200-50628400	Weak transcription	A549	lung
16	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
17	chr3:50608400-50625600	Weak transcription	NHDF-Ad	bronchial
18	chr3:50609200-50620800	Strong transcription	Brain Germinal Matrix	brain
19	chr3:50609800-50620600	Strong transcription	Fetal Brain Female	brain
20	chr3:50610000-50621400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:50610000-50623000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:50610200-50618000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:50610200-50618800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:50610200-50620400	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr3:50610200-50623600	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:50610200-50624400	Strong transcription	Fetal Stomach	stomach
27	chr3:50610200-50628000	Weak transcription	Stomach Mucosa	stomach
28	chr3:50610400-50615600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:50610400-50618600	Weak transcription	Right Atrium	heart
30	chr3:50610400-50622400	Weak transcription	GM12878-XiMat	blood
31	chr3:50610400-50623200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:50610400-50623200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr3:50610400-50628400	Weak transcription	HSMM	muscle
34	chr3:50610600-50616000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr3:50610600-50618200	Strong transcription	Adipose Nuclei	Adipose
36	chr3:50610600-50618400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:50610600-50627600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:50610800-50618000	Weak transcription	Fetal Heart	heart
39	chr3:50610800-50618400	Weak transcription	Psoas Muscle	Psoas
40	chr3:50611000-50617600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr3:50611000-50620600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:50611200-50618800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:50611200-50621600	Strong transcription	Thymus	Thymus
44	chr3:50611400-50621600	Strong transcription	Fetal Intestine Small	intestine
45	chr3:50611600-50618000	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:50611600-50618200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:50611600-50619200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:50611800-50618400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:50612000-50617800	Strong transcription	Ovary	ovary
50	chr3:50612200-50616000	Genic enhancers	Fetal Thymus	thymus

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