Variant report

Variant	rs16972620
Chromosome Location	chr15:75079840-75079841
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	IRF4	chr15:75079607-75081355	GM12878	blood:	n/a	n/a
2	FOXM1	chr15:75079358-75081791	GM12878	blood:	n/a	n/a
3	CREB1	chr15:75079691-75081604	GM12878	blood:	n/a	n/a
4	BCL3	chr15:75079694-75080568	GM12878	blood:	n/a	chr15:75080342-75080351
5	TCF12	chr15:75079723-75080458	GM12878	blood:	n/a	chr15:75080186-75080193
6	SPI1	chr15:75079235-75080757	GM12878	blood:	n/a	chr15:75080342-75080351 chr15:75080585-75080598
7	YY1	chr15:75079782-75080536	GM12891	blood:	n/a	n/a
8	RELA	chr15:75079731-75081849	GM18526	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
9	YY1	chr15:75079609-75080553	GM12878	blood:	n/a	n/a
10	CEBPB	chr15:75079784-75080127	GM12878	blood:	n/a	n/a
11	BCLAF1	chr15:75079284-75082025	GM12878	blood:	n/a	chr15:75081349-75081362 chr15:75080342-75080351
12	ETS1	chr15:75079663-75080717	GM12878	blood:	n/a	chr15:75080342-75080353 chr15:75080342-75080355 chr15:75080340-75080354
13	RELA	chr15:75078968-75083276	GM18951	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
14	MEF2A	chr15:75079477-75080696	GM12878	blood:	n/a	chr15:75079564-75079575 chr15:75079565-75079574
15	ATF2	chr15:75078945-75081778	GM12878	blood:	n/a	chr15:75079326-75079340
16	POLR2A	chr15:75077574-75083240	GM19193	blood:	n/a	n/a
17	NFATC1	chr15:75079098-75082965	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:75078871-75082774	GM12891	blood:	n/a	n/a
19	STAT3	chr15:75079696-75081648	GM12878	blood:	n/a	chr15:75081561-75081573
20	ZNF143	chr15:75079353-75080576	GM12878	blood:	n/a	chr15:75079454-75079472
21	SPI1	chr15:75079726-75079903	K562	blood:	n/a	n/a
22	POLR2A	chr15:75078541-75083313	GM12892	blood:	n/a	n/a
23	RCOR1	chr15:75079715-75080838	IMR90	lung:	n/a	n/a
24	POLR2A	chr15:75078876-75083272	GM12878	blood:	n/a	n/a
25	RELA	chr15:75078928-75083342	GM18505	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
26	ZNF263	chr15:75079269-75080344	K562	blood:	n/a	chr15:75079479-75079500
27	BHLHE40	chr15:75079621-75081908	GM12878	blood:	n/a	chr15:75081355-75081371
28	RELA	chr15:75079439-75082060	GM15510	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
29	POU2F2	chr15:75078933-75083247	GM12878	blood:	n/a	chr15:75081175-75081185 chr15:75081175-75081185 chr15:75081174-75081186 chr15:75081172-75081187 chr15:75081176-75081183 chr15:75081168-75081189 chr15:75081174-75081184 chr15:75081175-75081183 chr15:75081175-75081184 chr15:75081170-75081188 chr15:75081173-75081184
30	SPI1	chr15:75079659-75080564	HL-60	blood:	n/a	chr15:75080342-75080351
31	POLR2A	chr15:75078956-75083263	GM12892	blood:	n/a	n/a
32	CHD2	chr15:75079257-75083224	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:75079535-75083264	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:75076731-75083396	GM12892	blood:	n/a	n/a
35	BRCA1	chr15:75079767-75081462	GM12878	blood:	n/a	n/a
36	POLR2A	chr15:75072814-75083294	GM19099	blood:	n/a	n/a
37	POLR2A	chr15:75072482-75083351	GM12878	blood:	n/a	n/a
38	BCL11A	chr15:75079643-75080593	GM12878	blood:	n/a	chr15:75080342-75080351
39	POU2F2	chr15:75079637-75081601	GM12878	blood:	n/a	chr15:75081175-75081185 chr15:75081175-75081185 chr15:75081174-75081186 chr15:75081172-75081187 chr15:75081176-75081183 chr15:75081168-75081189 chr15:75081174-75081184 chr15:75081175-75081183 chr15:75081175-75081184 chr15:75081170-75081188 chr15:75081173-75081184
40	CHD1	chr15:75079224-75081883	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:75078570-75083275	GM18505	blood:	n/a	n/a
42	PAX5	chr15:75079740-75080457	GM12878	blood:	n/a	chr15:75080342-75080351
43	MAZ	chr15:75079154-75082852	GM12878	blood:	n/a	chr15:75082678-75082687 chr15:75081867-75081877
44	BCLAF1	chr15:75078912-75083306	GM12878	blood:	n/a	chr15:75081349-75081362 chr15:75080342-75080351
45	SPI1	chr15:75079672-75080052	GM12878	blood:	n/a	n/a
46	SP1	chr15:75079601-75080633	GM12878	blood:	n/a	n/a
47	NFIC	chr15:75079556-75080702	GM12878	blood:	n/a	n/a
48	ZEB1	chr15:75079766-75080537	GM12878	blood:	n/a	n/a
49	PAX5	chr15:75079757-75080007	GM12891	blood:	n/a	n/a
50	POLR2A	chr15:75079708-75080688	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75078437..75080336-chr15:75126473..75129418,2	MCF-7	breast:
2	chr15:75079479..75082400-chr15:75103794..75106182,2	MCF-7	breast:
3	chr15:75073170..75080511-chr15:75126432..75130376,7	MCF-7	breast:
4	chr15:75078025..75080593-chr15:75113459..75116440,2	K562	blood:
5	chr15:75078889..75080796-chr15:75108013..75111153,3	MCF-7	breast:
6	chr15:75079443..75082335-chr15:75197190..75199145,2	MCF-7	breast:
7	chr15:75078830..75080819-chr15:75135000..75137189,2	K562	blood:
8	chr15:75079215..75085047-chr15:75133215..75137478,7	MCF-7	breast:
9	chr15:74906678..74909061-chr15:75078128..75081929,4	MCF-7	breast:
10	chr15:75079725..75083728-chr15:75089989..75095483,10	MCF-7	breast:

Variant related genes	Relation type
CSK	TF binding region
ENSG00000179335	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000260919	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11553760	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12437562	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs16972381	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs16972486	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs16972628	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229729	0.89[ASN][1000 genomes]
rs35290121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58050869	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer 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	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75075600-75080800	Enhancers	Fetal Heart	heart
2	chr15:75075600-75083400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr15:75075800-75082000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr15:75076000-75080400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:75076000-75080600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:75076000-75080800	Enhancers	Fetal Brain Male	brain
7	chr15:75076200-75080000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:75076200-75080000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:75076200-75080000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:75076200-75080200	Enhancers	Psoas Muscle	Psoas
11	chr15:75076200-75080200	Enhancers	Stomach Mucosa	stomach
12	chr15:75076400-75080000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:75076400-75080000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:75076400-75082200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr15:75076400-75083200	Enhancers	Colon Smooth Muscle	Colon
16	chr15:75076400-75083400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr15:75076400-75083400	Genic enhancers	Fetal Stomach	stomach
18	chr15:75076400-75083400	Enhancers	Right Ventricle	heart
19	chr15:75076400-75084200	Enhancers	Spleen	Spleen
20	chr15:75076400-75085800	Enhancers	Left Ventricle	heart
21	chr15:75076600-75080400	Enhancers	Brain Germinal Matrix	brain
22	chr15:75076600-75080800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:75076600-75080800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:75076600-75081000	Genic enhancers	Fetal Intestine Large	intestine
25	chr15:75076600-75082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:75076600-75082600	Genic enhancers	NHEK	skin
27	chr15:75076600-75082800	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr15:75076600-75083400	Enhancers	Right Atrium	heart
29	chr15:75076600-75083400	Enhancers	HMEC	breast
30	chr15:75076600-75084800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:75076800-75080000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:75076800-75081600	Genic enhancers	Fetal Intestine Small	intestine
33	chr15:75076800-75083200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:75077200-75081000	Genic enhancers	K562	blood
35	chr15:75077200-75082200	Genic enhancers	Fetal Muscle Leg	muscle
36	chr15:75077600-75081800	Genic enhancers	Lung	lung
37	chr15:75077600-75083000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:75077600-75083000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:75077600-75083200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:75077800-75081200	Enhancers	Brain Substantia Nigra	brain
41	chr15:75077800-75082200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:75077800-75084400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:75077800-75092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:75078000-75080600	Weak transcription	Fetal Kidney	kidney
45	chr15:75078000-75081200	Enhancers	Liver	Liver
46	chr15:75078000-75081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:75078000-75082000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr15:75078000-75083400	Enhancers	Placenta	Placenta
49	chr15:75078000-75083400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr15:75078000-75083600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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