Variant report

Variant	rs7514402
Chromosome Location	chr1:146555392-146555393
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:146555353-146556785	IMR90	lung:	n/a	n/a
2	RDBP	chr1:146555360-146556389	K562	blood:	n/a	n/a
3	TAL1	chr1:146555099-146556455	K562	blood:	n/a	n/a
4	ZNF274	chr1:146555035-146556323	K562	blood:	n/a	n/a
5	POLR2A	chr1:146555307-146556790	GM12878	blood:	n/a	n/a
6	HEY1	chr1:146555085-146557466	K562	blood:	n/a	chr1:146556495-146556510
7	POLR2A	chr1:146555334-146556837	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:146555298-146557243	MCF10A-Er-Src	breast:	n/a	n/a
9	MAFF	chr1:146555019-146556810	K562	blood:	n/a	n/a
10	POLR2A	chr1:146555130-146557088	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr1:146555390-146556734	K562	blood:	n/a	n/a
12	GTF2F1	chr1:146555266-146556804	K562	blood:	n/a	n/a
13	POLR2A	chr1:146555354-146557241	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:146555187-146556948	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBL1XR1	chr1:146555162-146556848	K562	blood:	n/a	n/a
16	POLR2A	chr1:146555303-146557217	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:146555386-146557416	K562	blood:	n/a	n/a
18	POLR2A	chr1:146555328-146556789	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:146555386-146557019	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:146555355-146556810	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:146555353-146556869	GM12878	blood:	n/a	n/a
22	MAFK	chr1:146555317-146555489	HepG2	liver:	n/a	chr1:146555449-146555464
23	CEBPB	chr1:146555362-146556677	K562	blood:	n/a	n/a
24	POLR2A	chr1:146555391-146556808	GM12891	blood:	n/a	n/a
25	CHD2	chr1:146555292-146556706	K562	blood:	n/a	n/a
26	SIN3A	chr1:146555294-146556891	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:146555308..146557751-chr1:146572492..146574636,3	MCF-7	breast:
2	chr1:146555350..146556240-chr3:193852240..193853122,2	Hela-S3	cervix:
3	chr1:146554717..146557790-chr1:146713275..146715735,7	MCF-7	breast:
4	chr1:146554322..146557448-chr1:146695605..146698369,3	K562	blood:
5	chr1:146554504..146557399-chr1:146713775..146716499,4	MCF-7	breast:
6	chr1:146553836..146557884-chr1:146641755..146644199,5	MCF-7	breast:
7	chr1:146554548..146558121-chr1:149223419..149225403,4	MCF-7	breast:
8	chr1:146554384..146557759-chr1:149221710..149225398,8	K562	blood:
9	chr1:146554522..146557720-chr1:147805011..147808218,6	K562	blood:
10	chr1:146554412..146557592-chr1:149221795..149226039,8	K562	blood:
11	chr1:146555134..146556670-chr1:146623816..146625708,2	K562	blood:
12	chr1:146555358..146556038-chr7:2594809..2595422,2	Hela-S3	cervix:
13	chr1:146550590..146559110-chr1:146711930..146718078,31	K562	blood:
14	chr1:146552515..146557737-chr1:146711619..146718083,31	K562	blood:
15	chr1:146554115..146557849-chr1:146637949..146646936,17	MCF-7	breast:
16	chr1:146555129..146557611-chr1:146720507..146722463,2	K562	blood:
17	chr1:144531278..144537146-chr1:146553717..146557612,11	K562	blood:
18	chr1:146554326..146556624-chr1:149762818..149765682,2	K562	blood:
19	chr1:146502664..146505503-chr1:146555291..146557477,4	MCF-7	breast:
20	chr1:146554089..146558005-chr1:146638440..146645674,16	K562	blood:
21	chr1:146554322..146556284-chr1:146695615..146697996,2	K562	blood:
22	chr1:146554821..146557331-chr17:58468506..58470510,2	MCF-7	breast:
23	chr1:146554921..146557589-chr7:94462581..94464231,2	MCF-7	breast:
24	chr1:146554823..146556812-chr1:146593975..146596191,2	MCF-7	breast:
25	chr1:146554089..146558005-chr1:146640920..146646223,16	K562	blood:
26	chr1:144532709..144537146-chr1:146553385..146558827,17	K562	blood:

No data

Variant related genes	Relation type
ENSG00000230832	TF binding region
ENSG00000141371	Chromatin interaction
ENSG00000219807	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000131778	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000170832	Chromatin interaction
ENSG00000202408	Chromatin interaction
ENSG00000131781	Chromatin interaction
ENSG00000227242	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000233030	Chromatin interaction
ENSG00000106009	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10157765	0.80[ASN][1000 genomes]
rs10900313	0.86[ASN][1000 genomes]
rs21327	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3011806	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4528168	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4950357	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557929	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615558	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs636329	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs646703	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs692963	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9633428	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
4	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
7	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
8	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv946298	chr1:146510432-146557539	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
10	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription 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	110 gene(s)	inside rSNPs	diseases
15	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
16	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7514402	RP11-325P15.1	cis	lung	GTEx
rs7514402	NBPF13P	cis	lung	GTEx
rs7514402	NBPF13P	cis	Whole Blood	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146552200-146555600	Weak transcription	Right Atrium	heart
2	chr1:146552600-146555400	Weak transcription	Spleen	Spleen
3	chr1:146552600-146555600	Weak transcription	Pancreas	Pancrea
4	chr1:146555000-146555400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr1:146555000-146555600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
6	chr1:146555000-146555800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:146555000-146557200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:146555000-146557200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:146555200-146555400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr1:146555200-146555400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr1:146555200-146555400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr1:146555200-146555400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:146555200-146555400	Bivalent Enhancer	Primary B cells from cord blood	blood
14	chr1:146555200-146555400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:146555200-146555400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:146555200-146555400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
17	chr1:146555200-146555400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
18	chr1:146555200-146555400	Bivalent Enhancer	HepG2	liver
19	chr1:146555200-146555400	Enhancers	HMEC	breast
20	chr1:146555200-146555400	Flanking Active TSS	NHEK	skin
21	chr1:146555200-146555600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:146555200-146555600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:146555200-146555600	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:146555200-146555600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr1:146555200-146555600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
26	chr1:146555200-146555600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:146555200-146555600	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
28	chr1:146555200-146555600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:146555200-146555600	Bivalent Enhancer	Brain Substantia Nigra	brain
30	chr1:146555200-146555600	Bivalent Enhancer	Fetal Intestine Large	intestine
31	chr1:146555200-146555600	Flanking Active TSS	Hela-S3	cervix
32	chr1:146555200-146555600	Bivalent/Poised TSS	Osteobl	bone
33	chr1:146555200-146555800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr1:146555200-146555800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:146555200-146555800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:146555200-146555800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:146555200-146556000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:146555200-146556000	Flanking Active TSS	K562	blood
39	chr1:146555200-146556800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:146555200-146557200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:146555200-146557200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr1:146555200-146557400	Active TSS	HSMMtube	muscle

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