Variant report

Variant	rs3002452
Chromosome Location	chr14:105283727-105283728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:105280934-105283939	HepG2	liver:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:105283173..105285721-chr14:105343365..105345271,2	K562	blood:
2	chr14:105276873..105279342-chr14:105282954..105284515,2	K562	blood:
3	chr14:105280921..105283748-chr14:105368977..105371929,2	MCF-7	breast:
4	chr14:105282332..105284186-chr14:105286769..105289212,2	K562	blood:
5	chr14:105269532..105276799-chr14:105278912..105285805,20	K562	blood:
6	chr14:105262687..105269353-chr14:105280701..105285854,11	K562	blood:
7	chr14:105282326..105284059-chr14:105337774..105340057,2	MCF-7	breast:
8	chr14:105281237..105284085-chr14:105486215..105487992,2	MCF-7	breast:
9	chr14:105196164..105197690-chr14:105281072..105283961,2	MCF-7	breast:
10	chr14:105259095..105269353-chr14:105280422..105289302,26	K562	blood:
11	chr14:105281635..105284024-chr14:105340547..105342098,2	MCF-7	breast:
12	chr14:105234439..105237924-chr14:105282757..105285327,3	K562	blood:
13	chr14:105282292..105284225-chr14:105434347..105435910,2	MCF-7	breast:
14	chr14:105115276..105117715-chr14:105282961..105284901,2	MCF-7	breast:
15	chr14:105281444..105284186-chr14:105287475..105289212,2	K562	blood:
16	chr14:105282552..105286026-chr14:105289483..105293569,5	K562	blood:
17	chr14:105282636..105284181-chr14:105486257..105488392,2	MCF-7	breast:
18	chr14:105183762..105186592-chr14:105282456..105284032,2	MCF-7	breast:
19	chr14:105280824..105284770-chr14:105329671..105333393,8	MCF-7	breast:
20	chr14:105153182..105156067-chr14:105281278..105283744,4	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00638	TF binding region
ENSG00000170779	Chromatin interaction
ENSG00000099814	Chromatin interaction
ENSG00000258701	Chromatin interaction
ENSG00000142208	Chromatin interaction
ENSG00000259067	Chromatin interaction
ENSG00000179627	Chromatin interaction
ENSG00000185100	Chromatin interaction
ENSG00000203485	Chromatin interaction
ENSG00000258430	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10138512	0.98[ASN][1000 genomes]
rs10139525	1.00[ASN][1000 genomes]
rs10142116	1.00[ASN][1000 genomes]
rs12050408	0.97[ASN][1000 genomes]
rs12889174	0.83[AFR][1000 genomes]
rs12894160	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2498778	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2498779	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2498807	1.00[ASN][1000 genomes]
rs2498808	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2498809	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2498810	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35914118	0.97[ASN][1000 genomes]
rs8009473	0.81[AFR][1000 genomes]
rs8010024	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530812	chr14:104775571-105364883	Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription 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	98 gene(s)	inside rSNPs	diseases
2	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv2830002	chr14:105078251-105348552	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv902388	chr14:105092479-105311249	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
6	nsv902389	chr14:105092479-105366499	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv470677	chr14:105126354-105348552	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
10	nsv517038	chr14:105146579-105311249	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
11	nsv566057	chr14:105146579-105311249	Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer 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	69 gene(s)	inside rSNPs	diseases
12	nsv566060	chr14:105148655-105311249	Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Weak transcription 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 target site	66 gene(s)	inside rSNPs	diseases
13	nsv902404	chr14:105148655-105311249	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
14	nsv902405	chr14:105148655-105340643	Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv902409	chr14:105154105-105311249	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
16	nsv566063	chr14:105154105-105312935	Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
17	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
18	nsv902412	chr14:105238701-105361934	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
19	esv1836552	chr14:105246686-105348552	Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
20	nsv902413	chr14:105246686-105366499	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
21	esv1833474	chr14:105268228-105332154	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
22	nsv566092	chr14:105274086-105286331	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
23	nsv566093	chr14:105274093-105321835	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
24	esv1840298	chr14:105274292-105366499	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
25	nsv902416	chr14:105277209-105366499	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3002452	LINC00638	cis	Esophagus Mucosa	GTEx
rs3002452	LINC00638	cis	Nerve Tibial	GTEx
rs3002452	LINC00638	cis	Thyroid	GTEx
rs3002452	LINC00638	cis	lung	GTEx
rs3002452	LINC00638	cis	Artery Aorta	GTEx
rs3002452	LINC00638	cis	Esophagus Muscularis	GTEx
rs3002452	LINC00638	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105281200-105283800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr14:105281200-105283800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr14:105283000-105283800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr14:105283000-105283800	Flanking Active TSS	HepG2	liver
5	chr14:105283000-105284000	Flanking Active TSS	Dnd41	blood
6	chr14:105283200-105283800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr14:105283200-105283800	Active TSS	HSMM	muscle
8	chr14:105283200-105284000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:105283200-105284200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:105283200-105284600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:105283200-105287000	Weak transcription	Esophagus	oesophagus
12	chr14:105283200-105292200	Weak transcription	Gastric	stomach
13	chr14:105283400-105283800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:105283400-105283800	Enhancers	Primary hematopoietic stem cells	blood
15	chr14:105283400-105283800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:105283400-105283800	Enhancers	Brain Cingulate Gyrus	brain
17	chr14:105283400-105283800	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr14:105283400-105283800	Enhancers	Fetal Stomach	stomach
19	chr14:105283400-105284000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:105283400-105284000	Enhancers	Primary B cells from cord blood	blood
21	chr14:105283400-105284000	Enhancers	Primary B cells from peripheral blood	blood
22	chr14:105283400-105284000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr14:105283400-105284000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr14:105283400-105284000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr14:105283400-105284000	Enhancers	Adipose Nuclei	Adipose
26	chr14:105283400-105284000	Enhancers	Liver	Liver
27	chr14:105283400-105284000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr14:105283400-105284000	Enhancers	Colon Smooth Muscle	Colon
29	chr14:105283400-105284000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr14:105283400-105284000	Enhancers	Fetal Heart	heart
31	chr14:105283400-105284000	Enhancers	Fetal Muscle Leg	muscle
32	chr14:105283400-105284000	Enhancers	Placenta	Placenta
33	chr14:105283400-105284000	Enhancers	Left Ventricle	heart
34	chr14:105283400-105284000	Enhancers	Rectal Smooth Muscle	rectum
35	chr14:105283400-105284000	Enhancers	Spleen	Spleen
36	chr14:105283400-105284000	Enhancers	Osteobl	bone
37	chr14:105283400-105284200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr14:105283400-105284200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr14:105283400-105284200	Weak transcription	Fetal Intestine Small	intestine
40	chr14:105283400-105284200	Weak transcription	Fetal Kidney	kidney
41	chr14:105283400-105284200	Weak transcription	Fetal Lung	lung
42	chr14:105283400-105284200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr14:105283400-105284400	Weak transcription	A549	lung
44	chr14:105283400-105284600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr14:105283400-105284600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr14:105283400-105284800	Weak transcription	Fetal Intestine Large	intestine
47	chr14:105283400-105285000	Weak transcription	Lung	lung
48	chr14:105283400-105286800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr14:105283400-105286800	Weak transcription	HSMMtube	muscle
50	chr14:105283400-105286800	Weak transcription	HUVEC	blood vessel

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