Variant report

Variant	rs648514
Chromosome Location	chr3:52467263-52467264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52444856..52447738-chr3:52466597..52468559,2	K562	blood:
2	chr3:52460037..52468104-chr3:52477512..52481927,11	MCF-7	breast:
3	chr3:52463683..52467756-chr3:52469500..52473710,3	K562	blood:
4	chr3:52460730..52462242-chr3:52466014..52467861,2	K562	blood:

Variant related genes	Relation type
ENSG00000010318	Chromatin interaction
ENSG00000010319	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1060330	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs11716487	0.82[YRI][hapmap]
rs11717383	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs498946	0.81[YRI][hapmap]
rs610060	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs634382	0.82[YRI][hapmap]
rs6445358	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs730050	0.87[MEX][hapmap]
rs7614727	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs7622851	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS 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	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs648514	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs648514	SEMA3G	cis	parietal	SCAN
rs648514	DNAH1	cis	cerebellum	SCAN
rs648514	SEMA3G	cis	cerebellum	SCAN
rs648514	GNL3	cis	cerebellum	SCAN
rs648514	ITIH4	cis	parietal	SCAN
rs648514	GLYCTK	cis	parietal	SCAN
rs648514	NEK4	cis	parietal	SCAN
rs648514	RBM6	cis	parietal	SCAN
rs648514	RBM6	cis	cerebellum	SCAN
rs648514	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs648514	NT5DC2	cis	lymphoblastoid	seeQTL
rs648514	GNL3	cis	parietal	SCAN
rs648514	NEK4	cis	cerebellum	SCAN
rs648514	SPCS1	cis	parietal	SCAN
rs648514	NDUFAF3	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52445600-52471600	Weak transcription	Gastric	stomach
2	chr3:52446200-52467800	Weak transcription	Esophagus	oesophagus
3	chr3:52446400-52470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:52447000-52470200	Weak transcription	Fetal Lung	lung
5	chr3:52447200-52468000	Weak transcription	Colonic Mucosa	Colon
6	chr3:52447400-52467600	Weak transcription	NHEK	skin
7	chr3:52448600-52471200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:52450200-52478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:52454200-52467600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:52462800-52469200	Enhancers	Adipose Nuclei	Adipose
11	chr3:52462800-52469800	Enhancers	Placenta	Placenta
12	chr3:52462800-52473600	Enhancers	Fetal Muscle Leg	muscle
13	chr3:52463000-52469200	Enhancers	Fetal Muscle Trunk	muscle
14	chr3:52463000-52469200	Enhancers	Left Ventricle	heart
15	chr3:52463400-52467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:52463400-52467600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr3:52463400-52470400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:52463800-52468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52464400-52467600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:52464600-52468000	Enhancers	HepG2	liver
21	chr3:52464600-52477400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:52465000-52468600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:52465000-52468600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:52465200-52469200	Enhancers	Right Atrium	heart
25	chr3:52465600-52469200	Enhancers	Right Ventricle	heart
26	chr3:52465600-52470800	Enhancers	Fetal Heart	heart
27	chr3:52465800-52467600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:52466000-52468000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:52466000-52468200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:52466000-52468400	Enhancers	Fetal Stomach	stomach
31	chr3:52466000-52469000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:52466000-52469600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:52466000-52471400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:52466200-52468000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr3:52466400-52468600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52466400-52469400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:52466400-52473200	Enhancers	Spleen	Spleen
38	chr3:52466600-52467400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr3:52466800-52467400	Enhancers	HUVEC	blood vessel
40	chr3:52466800-52467600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:52466800-52467800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:52466800-52468200	Enhancers	HSMMtube	muscle
43	chr3:52467000-52467400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:52467000-52467400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:52467000-52467400	Weak transcription	Ovary	ovary
46	chr3:52467000-52468200	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr3:52467200-52467600	Weak transcription	Lung	lung
48	chr3:52467200-52467800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:52467200-52467800	Enhancers	Fetal Kidney	kidney

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