Variant report

Variant	rs1648301
Chromosome Location	chr15:45494017-45494018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45492131-45494103	GM12878	blood:	n/a	n/a
2	CHD2	chr15:45492283-45494186	GM12878	blood:	n/a	n/a
3	RELA	chr15:45492248-45494117	GM19099	blood:	n/a	chr15:45493570-45493579 chr15:45493570-45493579
4	EBF1	chr15:45493298-45494122	GM12878	blood:	n/a	n/a
5	BATF	chr15:45493725-45494207	GM12878	blood:	n/a	n/a
6	GTF3C2	chr15:45489873-45494042	Hela-S3	cervix:	n/a	n/a
7	MAZ	chr15:45492270-45494079	GM12878	blood:	n/a	n/a
8	RELA	chr15:45492260-45494091	GM10847	blood:	n/a	chr15:45493570-45493579 chr15:45493570-45493579
9	RUNX3	chr15:45492187-45494242	GM12878	blood:	n/a	n/a
10	EP300	chr15:45493296-45494142	GM12878	blood:	n/a	chr15:45494075-45494089
11	POLR2A	chr15:45492154-45494113	GM12878	blood:	n/a	n/a
12	RCOR1	chr15:45492282-45494081	GM12878	blood:	n/a	n/a
13	SP1	chr15:45493704-45494140	GM12878	blood:	n/a	n/a
14	GTF3C2	chr15:45492207-45494251	K562	blood:	n/a	n/a
15	MAFF	chr15:45494009-45494137	HepG2	liver:	n/a	n/a
16	POU2F2	chr15:45492397-45494161	GM12878	blood:	n/a	chr15:45493789-45493811
17	RUNX3	chr15:45492201-45494112	GM12878	blood:	n/a	n/a
18	ZNF143	chr15:45493765-45494047	GM12878	blood:	n/a	n/a
19	TBP	chr15:45492216-45494104	GM12878	blood:	n/a	n/a
20	RELA	chr15:45492313-45494059	GM19193	blood:	n/a	chr15:45493570-45493579 chr15:45493570-45493579
21	NFIC	chr15:45492150-45494180	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:45493673-45494028	GM12891	blood:	n/a	n/a
23	BCL11A	chr15:45493684-45494107	GM12878	blood:	n/a	chr15:45493966-45493975
24	BCL11A	chr15:45493656-45494078	GM12878	blood:	n/a	chr15:45493966-45493975
25	EP300	chr15:45492381-45494149	GM12878	blood:	n/a	chr15:45494075-45494089
26	SMC3	chr15:45493898-45494129	GM12878	blood:	n/a	n/a
27	PAX5	chr15:45492322-45494089	GM12878	blood:	n/a	chr15:45492851-45492869
28	SREBP2	chr15:45489970-45494276	GM12878	blood:	n/a	n/a
29	WRNIP1	chr15:45493865-45494256	GM12878	blood:	n/a	n/a
30	STAT3	chr15:45492222-45494150	GM12878	blood:	n/a	chr15:45493476-45493487 chr15:45493478-45493486
31	RELA	chr15:45492244-45494069	GM18951	blood:	n/a	chr15:45493570-45493579 chr15:45493570-45493579
32	CUX1	chr15:45493283-45494032	GM12878	blood:	n/a	n/a
33	BHLHE40	chr15:45492222-45494159	GM12878	blood:	n/a	n/a
34	MXI1	chr15:45492212-45494117	GM12878	blood:	n/a	n/a
35	TBL1XR1	chr15:45492255-45494049	GM12878	blood:	n/a	n/a
36	POLR2A	chr15:45492279-45494036	GM12892	blood:	n/a	n/a
37	BHLHE40	chr15:45492260-45494028	K562	blood:	n/a	n/a
38	EP300	chr15:45492340-45494096	GM12878	blood:	n/a	chr15:45494075-45494089
39	MTA3	chr15:45492089-45494204	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45478077..45482452-chr15:45491020..45494377,5	MCF-7	breast:
2	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:
3	chr15:45464999..45466823-chr15:45492725..45494272,2	K562	blood:
4	chr15:45493253..45495607-chr15:45694426..45696533,2	K562	blood:
5	chr15:45464999..45466823-chr15:45492725..45494339,3	K562	blood:
6	chr15:45457925..45460364-chr15:45492288..45495049,4	MCF-7	breast:
7	chr15:45491756..45494677-chr15:45570318..45572091,2	MCF-7	breast:

Variant related genes	Relation type
SHF	TF binding region
ENSG00000259932	TF binding region
ENSG00000260035	TF binding region
ENSG00000138606	Chromatin interaction
ENSG00000259520	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000259539	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10450971	0.94[ASN][1000 genomes]
rs12440127	0.94[ASN][1000 genomes]
rs12898733	0.92[ASN][1000 genomes]
rs1611896	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1617207	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1625404	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1625779	0.91[ASN][1000 genomes]
rs1628717	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632144	0.91[ASN][1000 genomes]
rs1648280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1648284	0.92[ASN][1000 genomes]
rs1648288	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648290	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs1648291	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648292	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1648296	0.92[ASN][1000 genomes]
rs1648297	0.83[ASN][1000 genomes]
rs1648298	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1648299	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648314	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs1648315	0.90[ASN][1000 genomes]
rs16940558	1.00[GIH][hapmap]
rs16941118	0.92[GIH][hapmap]
rs16941127	0.92[GIH][hapmap]
rs16941245	0.92[GIH][hapmap]
rs1706765	0.94[JPT][hapmap]
rs1706779	1.00[JPT][hapmap]
rs1706819	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs1706823	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1706828	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[ASN][1000 genomes]
rs1706833	0.97[ASN][1000 genomes]
rs1706836	0.97[ASN][1000 genomes]
rs1719249	0.92[GIH][hapmap]
rs2277611	1.00[TSI][hapmap]
rs2292468	0.83[JPT][hapmap]
rs2413777	0.94[ASN][1000 genomes]
rs2458238	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2458240	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458241	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[ASN][1000 genomes]
rs2467839	0.91[ASN][1000 genomes]
rs2668738	0.93[ASN][1000 genomes]
rs2668750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899376	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs2899377	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4775824	0.94[ASN][1000 genomes]
rs58701250	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167481	0.94[ASN][1000 genomes]
rs7173715	1.00[GIH][hapmap]
rs732622	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039041	1.00[GIH][hapmap]
rs938129	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs938130	0.91[ASN][1000 genomes]
rs9972443	0.92[GIH][hapmap]

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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45490200-45494400	Active TSS	Fetal Brain Female	brain
2	chr15:45492000-45494200	Active TSS	Stomach Smooth Muscle	stomach
3	chr15:45493400-45494200	Active TSS	Primary hematopoietic stem cells	blood
4	chr15:45493400-45495000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:45493400-45495000	Weak transcription	Aorta	Aorta
6	chr15:45493400-45495400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:45493400-45495400	Weak transcription	Ovary	ovary
8	chr15:45493400-45497000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:45493600-45494200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr15:45493600-45494200	Flanking Active TSS	GM12878-XiMat	blood
11	chr15:45493600-45494400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:45493600-45495000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:45493600-45495200	Weak transcription	Osteobl	bone
14	chr15:45493600-45495400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:45493600-45495400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:45493600-45495400	Weak transcription	Left Ventricle	heart
17	chr15:45493600-45496000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:45493600-45497000	Weak transcription	HSMMtube	muscle
19	chr15:45493600-45497200	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:45493600-45508000	Weak transcription	Right Atrium	heart
21	chr15:45493800-45494200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr15:45493800-45494200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr15:45493800-45494200	Enhancers	Primary B cells from cord blood	blood
24	chr15:45493800-45494200	Enhancers	Primary B cells from peripheral blood	blood
25	chr15:45493800-45494200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:45493800-45494200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr15:45493800-45494200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:45493800-45494200	Enhancers	Brain Anterior Caudate	brain
29	chr15:45493800-45494200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:45493800-45494200	Enhancers	Duodenum Mucosa	Duodenum
31	chr15:45493800-45494400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:45493800-45494400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr15:45493800-45494400	Flanking Active TSS	HepG2	liver
34	chr15:45493800-45494600	Weak transcription	Brain Substantia Nigra	brain
35	chr15:45493800-45495000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:45493800-45495600	Weak transcription	Adipose Nuclei	Adipose
37	chr15:45493800-45497000	Weak transcription	Stomach Mucosa	stomach
38	chr15:45494000-45494200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:45494000-45494200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr15:45494000-45494200	Enhancers	Dnd41	blood
41	chr15:45494000-45494200	Enhancers	Hela-S3	cervix
42	chr15:45494000-45494200	Enhancers	K562	blood
43	chr15:45494000-45494200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr15:45494000-45494400	Enhancers	Colonic Mucosa	Colon
45	chr15:45494000-45495600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr15:45494000-45496200	Enhancers	Liver	Liver
47	chr15:45494000-45497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:45494000-45497000	Weak transcription	Fetal Intestine Small	intestine
49	chr15:45494000-45497200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:45494000-45497200	Weak transcription	Brain Hippocampus Middle	brain

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