Variant report

Variant	rs74012259
Chromosome Location	chr15:41601743-41601744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41601722..41603239-chr15:41610507..41613182,2	K562	blood:
2	chr15:41574968..41578367-chr15:41600315..41603711,4	K562	blood:
3	chr15:41601722..41604409-chr15:41611682..41614263,2	K562	blood:
4	chr15:41579631..41582972-chr15:41599254..41603170,4	K562	blood:
5	chr15:41600052..41601763-chr15:41618801..41620323,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC012652.1.1-1	chr15:41600918-41601901	ENSG00000247556

No data

Variant related genes	Relation type
ENSG00000247556	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2918464	1.00[AMR][1000 genomes]
rs2947487	1.00[AMR][1000 genomes]
rs2947490	1.00[AMR][1000 genomes]
rs35123814	0.98[AFR][1000 genomes]
rs36124939	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55643943	0.82[AFR][1000 genomes]
rs55838056	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56140669	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56687496	1.00[AMR][1000 genomes]
rs57958502	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58165973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58218403	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59034095	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59073406	1.00[AMR][1000 genomes]
rs59343255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59659337	1.00[AMR][1000 genomes]
rs59850482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61602493	1.00[AMR][1000 genomes]
rs692377	1.00[AMR][1000 genomes]
rs7162242	0.80[AFR][1000 genomes]
rs7168916	1.00[AMR][1000 genomes]
rs7172892	1.00[AMR][1000 genomes]
rs74012258	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012264	1.00[AMR][1000 genomes]
rs74012273	0.85[AFR][1000 genomes]
rs74012275	0.86[AFR][1000 genomes]
rs74012276	0.91[AFR][1000 genomes]
rs8025218	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8028208	0.91[AFR][1000 genomes]
rs8029815	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8032010	1.00[AMR][1000 genomes]
rs8032335	1.00[AMR][1000 genomes]
rs8035341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8038086	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8038185	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8039815	0.91[AFR][1000 genomes]
rs8041170	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9745301	1.00[AMR][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	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	esv14767	chr15:41595813-41619355	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41577400-41610600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41577600-41606400	Weak transcription	Stomach Mucosa	stomach
3	chr15:41579200-41612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41580600-41603200	Weak transcription	Psoas Muscle	Psoas
5	chr15:41581200-41602200	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:41581200-41602600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:41581200-41604800	Weak transcription	Gastric	stomach
8	chr15:41581200-41605000	Weak transcription	Brain Substantia Nigra	brain
9	chr15:41581200-41607000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:41581200-41609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
12	chr15:41581400-41605000	Weak transcription	HMEC	breast
13	chr15:41581400-41610400	Weak transcription	NHLF	lung
14	chr15:41581600-41601800	Weak transcription	Fetal Lung	lung
15	chr15:41581600-41623600	Weak transcription	Fetal Kidney	kidney
16	chr15:41583200-41623600	Weak transcription	HSMM	muscle
17	chr15:41583800-41613000	Weak transcription	Right Ventricle	heart
18	chr15:41584000-41604800	Weak transcription	Aorta	Aorta
19	chr15:41585000-41602800	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:41585600-41623600	Weak transcription	Primary B cells from cord blood	blood
21	chr15:41587200-41606800	Weak transcription	Fetal Heart	heart
22	chr15:41587600-41623000	Weak transcription	NHEK	skin
23	chr15:41589400-41601800	Weak transcription	K562	blood
24	chr15:41589400-41603600	Weak transcription	Spleen	Spleen
25	chr15:41589400-41604800	Weak transcription	Pancreas	Pancrea
26	chr15:41589600-41604800	Weak transcription	Lung	lung
27	chr15:41589600-41624000	Weak transcription	Esophagus	oesophagus
28	chr15:41590200-41601800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:41590200-41609200	Weak transcription	Colonic Mucosa	Colon
30	chr15:41590200-41623600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:41590600-41601800	Weak transcription	Primary T cells from cord blood	blood
32	chr15:41590600-41602000	Weak transcription	Brain Germinal Matrix	brain
33	chr15:41590600-41603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:41590600-41606800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:41590600-41623000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:41590800-41623000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:41591000-41606600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:41591200-41605000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:41591200-41623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:41591200-41624000	Weak transcription	HSMMtube	muscle
41	chr15:41591600-41601800	Weak transcription	Left Ventricle	heart
42	chr15:41591600-41602400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:41591600-41606600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:41591600-41611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:41591600-41623200	Weak transcription	HUVEC	blood vessel
46	chr15:41591800-41603200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:41591800-41624000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:41592000-41601800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:41592000-41618400	Weak transcription	Fetal Brain Female	brain
50	chr15:41592400-41602000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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