Variant report

Variant	rs13326165
Chromosome Location	chr3:52532118-52532119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52530625..52532525-chr3:52540604..52543562,2	MCF-7	breast:
2	chr3:52528800..52530920-chr3:52531153..52533413,2	MCF-7	breast:
3	chr3:52527621..52529302-chr3:52531817..52533690,2	K562	blood:
4	chr3:52532062..52534916-chr3:52535199..52537993,2	K562	blood:
5	chr3:52531295..52534156-chr3:52543396..52545644,2	K562	blood:

Variant related genes	Relation type
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11709658	1.00[JPT][hapmap]
rs13066389	1.00[ASN][1000 genomes]
rs13066644	1.00[ASN][1000 genomes]
rs34735556	0.82[ASN][1000 genomes]
rs35225119	0.82[ASN][1000 genomes]
rs35272104	0.82[ASN][1000 genomes]
rs35325270	1.00[ASN][1000 genomes]
rs35371456	1.00[ASN][1000 genomes]
rs4687545	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs67749743	1.00[ASN][1000 genomes]
rs758801	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs758802	1.00[ASN][1000 genomes]
rs7614424	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7644763	0.90[ASN][1000 genomes]

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	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
3	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
4	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
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	63 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HDL cholesterol	24097068	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13326165	ITIH4	cis	cerebellum	SCAN
rs13326165	NT5DC2	cis	parietal	SCAN
rs13326165	DNAH1	cis	parietal	SCAN
rs13326165	ITIH4	cis	parietal	SCAN
rs13326165	ITIH3	cis	parietal	SCAN
rs13326165	MUSTN1	cis	cerebellum	SCAN
rs13326165	DNAH1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52508000-52532200	Weak transcription	K562	blood
2	chr3:52513400-52541400	Weak transcription	A549	lung
3	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
4	chr3:52527000-52532400	Weak transcription	GM12878-XiMat	blood
5	chr3:52527000-52538000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:52527000-52540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52527400-52532600	Weak transcription	Stomach Mucosa	stomach
8	chr3:52527800-52532800	Weak transcription	Primary T cells from cord blood	blood
9	chr3:52527800-52533200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:52527800-52533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52528000-52534800	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:52528600-52533600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr3:52529200-52533000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:52529200-52537400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:52529400-52532200	Active TSS	Brain Hippocampus Middle	brain
16	chr3:52530000-52537600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:52530000-52538800	Weak transcription	Gastric	stomach
18	chr3:52530200-52537600	Weak transcription	Pancreas	Pancrea
19	chr3:52530200-52551800	Weak transcription	Esophagus	oesophagus
20	chr3:52530400-52532200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:52530400-52552400	Weak transcription	Brain Substantia Nigra	brain
22	chr3:52530600-52532400	Weak transcription	NHLF	lung
23	chr3:52530600-52532600	Weak transcription	Colonic Mucosa	Colon
24	chr3:52530600-52535400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:52530800-52532200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:52530800-52532400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:52530800-52532800	Weak transcription	Liver	Liver
29	chr3:52530800-52537600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:52530800-52548200	Weak transcription	Right Ventricle	heart
31	chr3:52530800-52551600	Weak transcription	Fetal Intestine Small	intestine
32	chr3:52531000-52532200	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:52531000-52532200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:52531000-52532200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:52531000-52533000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:52531000-52535600	Weak transcription	Lung	lung
37	chr3:52531000-52547600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:52531400-52532600	Enhancers	Adipose Nuclei	Adipose
39	chr3:52531600-52532400	Enhancers	Spleen	Spleen
40	chr3:52531600-52533400	Enhancers	Brain Anterior Caudate	brain
41	chr3:52531600-52533600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:52531600-52533600	Enhancers	Primary B cells from cord blood	blood
43	chr3:52531800-52532200	Flanking Active TSS	Placenta	Placenta
44	chr3:52531800-52532200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr3:52531800-52532400	Enhancers	Fetal Stomach	stomach
46	chr3:52531800-52532800	Genic enhancers	HUVEC	blood vessel
47	chr3:52531800-52533000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:52531800-52533000	Enhancers	NH-A	brain
49	chr3:52531800-52533200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:52531800-52533200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links