Variant report

Variant	rs7048
Chromosome Location	chr15:43620073-43620074
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43619415-43621038	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:43619084-43620089	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr15:43618471-43623574	GM12891	blood:	n/a	n/a
4	POLR2A	chr15:43620054-43620346	HepG2	liver:	n/a	n/a
5	POLR2A	chr15:43617884-43623229	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:43618045-43620940	K562	blood:	n/a	n/a
7	POLR2A	chr15:43619431-43623219	K562	blood:	n/a	n/a
8	POLR2A	chr15:43620058-43623582	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr15:43618735-43620944	K562	blood:	n/a	n/a
10	POLR2A	chr15:43617486-43620882	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr15:43619221-43621507	HepG2	liver:	n/a	n/a
12	POLR2A	chr15:43619223-43620152	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:43620029-43620440	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr15:43619480-43620093	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr15:43617177-43620881	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr15:43620050-43621275	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:43397435..43400079-chr15:43619938..43624138,3	K562	blood:
2	chr15:43586330..43589415-chr15:43618040..43621005,4	K562	blood:
3	chr15:43618581..43624264-chr15:43661265..43664929,7	MCF-7	breast:
4	chr15:43478134..43480191-chr15:43618410..43620274,2	K562	blood:
5	chr15:43618584..43620563-chr15:43643035..43645762,2	K562	blood:
6	chr15:43586588..43588941-chr15:43618040..43620629,3	K562	blood:
7	chr15:43606393..43608534-chr15:43619037..43620672,2	MCF-7	breast:
8	chr15:43584770..43587744-chr15:43618210..43620882,2	MCF-7	breast:
9	chr15:43619535..43624096-chr15:43662038..43665421,4	K562	blood:
10	chr15:43571338..43574214-chr15:43618657..43622685,4	K562	blood:
11	chr15:43605237..43606957-chr15:43618740..43620246,2	K562	blood:
12	chr15:43618225..43620863-chr15:43639470..43641474,2	K562	blood:

No data

Variant related genes	Relation type
ADAL	TF binding region
ENSG00000140265	Chromatin interaction
ENSG00000137822	Chromatin interaction
ENSG00000166946	Chromatin interaction
ENSG00000159459	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10518812	0.82[ASW][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap]
rs12899865	0.90[ASW][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs12908460	0.82[AFR][1000 genomes]
rs12911569	0.83[AFR][1000 genomes]
rs12911740	0.90[ASW][hapmap];0.81[GIH][hapmap]
rs12912744	0.82[ASW][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap]
rs16957680	0.90[ASW][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap]
rs16957715	0.90[ASW][hapmap];0.81[GIH][hapmap]
rs17780920	0.82[ASW][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap]
rs34515241	0.83[AFR][1000 genomes]
rs34591748	0.91[AFR][1000 genomes]
rs35681736	0.86[AFR][1000 genomes]
rs3862138	0.81[GIH][hapmap];0.87[YRI][hapmap]
rs7173383	0.90[ASW][hapmap];0.81[GIH][hapmap]
rs7176923	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7177146	0.90[ASW][hapmap];0.81[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap]
rs7180812	1.00[ASW][hapmap];0.80[LWK][hapmap];0.83[MKK][hapmap]
rs7181634	0.82[ASW][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap]
rs72707530	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7048	TTBK2	cis	cerebellum	SCAN
rs7048	ZNF690	cis	multi-tissue	Pritchard
rs7048	ZSCAN29	cis	multi-tissue	Pritchard
rs7048	ZSCAN29	cis	lymphoblastoid	seeQTL
rs7048	CASC4	cis	cerebellum	SCAN
rs7048	LCMT2	cis	cerebellum	SCAN
rs7048	GCHFR	cis	cerebellum	SCAN
rs7048	ADAL	cis	cerebellum	SCAN
rs7048	LCMT2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43609000-43620200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:43611600-43620200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:43613000-43620600	Weak transcription	Right Atrium	heart
4	chr15:43613600-43620200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:43615000-43621000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:43615600-43620600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:43615800-43620600	Weak transcription	Brain Substantia Nigra	brain
8	chr15:43616400-43620600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:43616400-43620600	Weak transcription	HSMM	muscle
10	chr15:43616800-43620200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:43616800-43620400	Weak transcription	Fetal Intestine Large	intestine
12	chr15:43616800-43620600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:43616800-43620600	Weak transcription	Fetal Brain Male	brain
14	chr15:43617000-43620600	Weak transcription	Fetal Lung	lung
15	chr15:43617000-43621200	Weak transcription	Osteobl	bone
16	chr15:43617200-43620600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:43617200-43620800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:43617400-43620600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:43617600-43620600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:43617600-43620600	Weak transcription	A549	lung
21	chr15:43617800-43620200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:43617800-43620400	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:43617800-43620600	Weak transcription	NHLF	lung
24	chr15:43617800-43620800	Enhancers	Psoas Muscle	Psoas
25	chr15:43618000-43620400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:43618000-43620600	Weak transcription	Small Intestine	intestine
27	chr15:43618000-43620600	Weak transcription	GM12878-XiMat	blood
28	chr15:43618200-43620400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:43618200-43620600	Weak transcription	Gastric	stomach
30	chr15:43618200-43620600	Weak transcription	HMEC	breast
31	chr15:43618200-43620800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:43618200-43621400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:43618400-43620200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:43618400-43620600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr15:43618400-43620800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:43618600-43620600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:43618600-43620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:43618600-43620600	Weak transcription	Adipose Nuclei	Adipose
39	chr15:43618600-43620600	Weak transcription	Left Ventricle	heart
40	chr15:43618800-43620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:43618800-43620600	Weak transcription	NHEK	skin
42	chr15:43619000-43620600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:43619000-43620800	Weak transcription	Lung	lung
44	chr15:43619200-43620400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:43619200-43620600	Weak transcription	Placenta	Placenta
46	chr15:43619200-43620600	Weak transcription	Fetal Stomach	stomach
47	chr15:43619200-43621200	Weak transcription	HSMMtube	muscle
48	chr15:43619400-43620400	Weak transcription	Fetal Thymus	thymus
49	chr15:43619400-43620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr15:43619400-43620800	Genic enhancers	K562	blood

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