Variant report

Variant	rs4001330
Chromosome Location	chr4:119519318-119519319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10004322	0.87[ASN][1000 genomes]
rs10022024	0.87[ASN][1000 genomes]
rs10031029	1.00[ASN][1000 genomes]
rs10857060	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11734153	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12331454	0.84[ASN][1000 genomes]
rs12651650	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13137401	0.87[ASN][1000 genomes]
rs2389780	0.87[ASN][1000 genomes]
rs34016523	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34766719	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35731099	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35890030	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6855978	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71610209	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610213	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71610221	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72676188	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7656990	0.87[ASN][1000 genomes]
rs7669896	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7689541	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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	28 gene(s)	inside rSNPs	diseases
3	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv980251	chr4:119510579-119563981	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4001330	RP11-384K6.2	cis	Thyroid	GTEx
rs4001330	RP11-384K6.6	cis	Esophagus Mucosa	GTEx
rs4001330	RP11-384K6.6	cis	Adipose Subcutaneous	GTEx
rs4001330	RP11-384K6.6	cis	Artery Tibial	GTEx
rs4001330	RP11-384K6.2	cis	Nerve Tibial	GTEx
rs4001330	RP11-384K6.6	cis	Thyroid	GTEx
rs4001330	RP11-384K6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4001330	RP11-384K6.2	cis	Artery Tibial	GTEx
rs4001330	RP11-384K6.2	cis	Whole Blood	GTEx
rs4001330	RP11-384K6.6	cis	lung	GTEx
rs4001330	RP11-384K6.6	cis	Nerve Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119513400-119521800	Weak transcription	Colonic Mucosa	Colon
2	chr4:119513400-119522800	Weak transcription	Small Intestine	intestine
3	chr4:119513400-119527800	Weak transcription	Brain Substantia Nigra	brain
4	chr4:119513400-119528200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:119513400-119528400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:119513400-119534800	Weak transcription	Primary B cells from cord blood	blood
7	chr4:119513400-119551400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:119513400-119554000	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:119513400-119554800	Weak transcription	Ovary	ovary
10	chr4:119513400-119557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:119513600-119521000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:119513600-119521800	Weak transcription	HUVEC	blood vessel
13	chr4:119513600-119522200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:119513600-119524000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:119513600-119526400	Weak transcription	Left Ventricle	heart
16	chr4:119513600-119526600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:119513600-119526600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:119513600-119526600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:119513600-119526800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:119513600-119527000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:119513600-119527200	Weak transcription	Brain Germinal Matrix	brain
22	chr4:119513600-119528000	Weak transcription	HSMMtube	muscle
23	chr4:119513600-119529000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:119513600-119530600	Weak transcription	Primary T cells from cord blood	blood
25	chr4:119513600-119536800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:119513600-119539200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:119513600-119549200	Weak transcription	Esophagus	oesophagus
28	chr4:119513600-119550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:119513600-119551000	Weak transcription	Pancreas	Pancrea
30	chr4:119513600-119551600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:119513600-119552400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:119513600-119552400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:119513600-119552400	Weak transcription	Fetal Brain Female	brain
34	chr4:119513600-119552400	Weak transcription	Lung	lung
35	chr4:119513600-119552400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:119513600-119554000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:119513600-119555800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:119513600-119559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:119513800-119519400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:119513800-119526600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:119513800-119526800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:119513800-119527400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:119513800-119551200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:119513800-119552400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:119513800-119555000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:119513800-119556000	Weak transcription	Fetal Lung	lung
47	chr4:119517400-119526200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:119518000-119519400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr4:119518000-119520600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:119518000-119521200	Strong transcription	Adipose Nuclei	Adipose

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