Variant report

Variant	rs2582521
Chromosome Location	chr14:105310677-105310678
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:105218316..105220941-chr14:105310362..105313289,2	MCF-7	breast:
2	chr14:105308114..105313218-chr14:105327481..105332918,6	MCF-7	breast:
3	chr14:105309612..105312495-chr14:105330781..105333618,2	K562	blood:
4	chr14:105309392..105312329-chr14:105316131..105318426,2	K562	blood:
5	chr14:105309593..105311570-chr14:105314429..105316740,2	K562	blood:
6	chr14:105292878..105295272-chr14:105309126..105311348,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099814	Chromatin interaction
ENSG00000184990	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10130149	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10130338	0.81[ASN][1000 genomes]
rs10138387	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10149533	0.82[ASN][1000 genomes]
rs11625588	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11629188	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12101186	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12878750	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12889174	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12889498	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12889599	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12890464	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12895703	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2396455	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2582515	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2582516	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2582519	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2582520	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2841211	0.83[AMR][1000 genomes]
rs2841284	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28562928	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2919620	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2919621	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001409	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34149633	0.82[ASN][1000 genomes]
rs36029729	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4264330	0.81[ASN][1000 genomes]
rs4264331	0.81[ASN][1000 genomes]
rs66987285	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67906390	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8009473	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8010024	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 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	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
23	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
24	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
25	nsv511540	chr14:105285159-105314093	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	nsv456456	chr14:105285159-105412541	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
27	nsv566099	chr14:105285159-105412541	Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers 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	38 gene(s)	inside rSNPs	diseases
28	esv1793916	chr14:105292942-105321643	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
29	esv1825507	chr14:105292942-105321643	Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2582521	LINC00638	cis	lung	GTEx
rs2582521	LINC00638	cis	Thyroid	GTEx
rs2582521	LINC00638	cis	Nerve Tibial	GTEx
rs2582521	LINC00638	cis	Whole Blood	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105309600-105310800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr14:105309600-105310800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr14:105309600-105310800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr14:105309600-105310800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr14:105309600-105310800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:105309600-105310800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr14:105309600-105310800	Bivalent/Poised TSS	Colonic Mucosa	Colon
8	chr14:105309600-105311000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:105309600-105311000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr14:105309600-105311000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
11	chr14:105309600-105311200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
12	chr14:105309600-105311400	Active TSS	Brain Angular Gyrus	brain
13	chr14:105309600-105311400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
14	chr14:105309800-105310800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:105309800-105310800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:105309800-105310800	Active TSS	Aorta	Aorta
17	chr14:105309800-105310800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
18	chr14:105309800-105310800	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
19	chr14:105309800-105310800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
20	chr14:105309800-105310800	Active TSS	Right Atrium	heart
21	chr14:105309800-105310800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
22	chr14:105309800-105311000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr14:105309800-105311000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr14:105309800-105311000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr14:105309800-105311000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:105309800-105311000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
27	chr14:105309800-105311000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr14:105309800-105311200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr14:105309800-105311200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr14:105309800-105311200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr14:105309800-105311200	Bivalent Enhancer	Fetal Brain Male	brain
32	chr14:105309800-105311400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:105309800-105311400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
34	chr14:105310000-105310800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr14:105310000-105310800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
36	chr14:105310000-105310800	Flanking Active TSS	Pancreas	Pancrea
37	chr14:105310000-105311000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr14:105310000-105311000	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr14:105310000-105311200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
40	chr14:105310000-105311200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr14:105310000-105311200	Bivalent Enhancer	Fetal Heart	heart
42	chr14:105310000-105311200	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr14:105310000-105311600	Bivalent Enhancer	Spleen	Spleen
44	chr14:105310200-105310800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
45	chr14:105310200-105310800	Bivalent Enhancer	Fetal Intestine Small	intestine
46	chr14:105310200-105311000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr14:105310200-105311000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
48	chr14:105310200-105311200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:105310200-105311200	Bivalent Enhancer	Brain Substantia Nigra	brain
50	chr14:105310400-105310800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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