Variant report

Variant	rs6497005
Chromosome Location	chr15:93424895-93424896
allele	G/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	ZC3H11A	chr15:93424871-93426167	K562	blood:	n/a	n/a
2	POLR2A	chr15:93424491-93428698	GM12891	blood:	n/a	n/a
3	REST	chr15:93424890-93425702	A549	lung:	n/a	chr15:93425104-93425118
4	POLR2A	chr15:93424514-93426185	U87	brain:	n/a	n/a
5	MAFK	chr15:93424682-93424964	K562	blood:	n/a	n/a
6	POLR2A	chr15:93424787-93425776	U87	brain:	n/a	n/a
7	ZMIZ1	chr15:93424784-93426272	K562	blood:	n/a	n/a
8	TEAD4	chr15:93424718-93426192	K562	blood:	n/a	n/a
9	REST	chr15:93424836-93430889	H1-neurons	neurons:	n/a	chr15:93425104-93425118
10	POLR2A	chr15:93424349-93427371	GM12878	blood:	n/a	n/a
11	MYC	chr15:93424553-93426652	K562	blood:	n/a	n/a
12	POLR2A	chr15:93424751-93425824	SK-N-MC	brain:	n/a	n/a
13	NFATC1	chr15:93424857-93425790	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:93424642-93426415	PFSK-1	brain:	n/a	n/a
15	IRF1	chr15:93424557-93426511	K562	blood:	n/a	chr15:93424872-93424882 chr15:93425619-93425628 chr15:93424871-93424882 chr15:93424762-93424773 chr15:93424763-93424777 chr15:93424763-93424773 chr15:93424759-93424773 chr15:93424864-93424876 chr15:93424964-93424971 chr15:93425413-93425423 chr15:93424868-93424882 chr15:93424757-93424774 chr15:93425409-93425423
16	ZNF143	chr15:93424770-93426199	K562	blood:	n/a	chr15:93425999-93426017
17	POLR2A	chr15:93424850-93425717	GM12891	blood:	n/a	n/a
18	MXI1	chr15:93424871-93427275	IMR90	lung:	n/a	chr15:93425142-93425157
19	EP300	chr15:93424821-93426198	A549	lung:	n/a	chr15:93424934-93424948 chr15:93425381-93425391 chr15:93425408-93425422
20	IRF1	chr15:93424450-93426224	K562	blood:	n/a	chr15:93424872-93424882 chr15:93425619-93425628 chr15:93424871-93424882 chr15:93424762-93424773 chr15:93424763-93424777 chr15:93424763-93424773 chr15:93424759-93424773 chr15:93424864-93424876 chr15:93424964-93424971 chr15:93425413-93425423 chr15:93424868-93424882 chr15:93424757-93424774 chr15:93425409-93425423
21	POLR2A	chr15:93424424-93426225	PANC-1	pancreas:	n/a	n/a
22	MTA3	chr15:93424609-93425785	GM12878	blood:	n/a	n/a
23	BCL3	chr15:93424683-93426269	A549	lung:	n/a	chr15:93426000-93426013 chr15:93425998-93426007 chr15:93426184-93426197 chr15:93424764-93424773
24	HEY1	chr15:93424398-93426515	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:93424473-93427055	K562	blood:	n/a	n/a
26	POLR2A	chr15:93424663-93427256	GM19099	blood:	n/a	n/a
27	POLR2A	chr15:93424690-93427323	GM12892	blood:	n/a	n/a
28	POLR2A	chr15:93424268-93428846	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr15:93424531-93429178	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr15:93424609-93425873	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:93424853-93427333	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:93424470-93426608	HepG2	liver:	n/a	n/a
33	HCFC1	chr15:93424356-93427940	Hela-S3	cervix:	n/a	n/a
34	HCFC1	chr15:93424869-93426407	K562	blood:	n/a	n/a
35	POLR2A	chr15:93424589-93425761	HepG2	liver:	n/a	n/a
36	BCL3	chr15:93424747-93425837	A549	lung:	n/a	chr15:93424764-93424773
37	TAL1	chr15:93424831-93426254	K562	blood:	n/a	n/a
38	SIN3AK20	chr15:93424787-93427602	MCF-7	breast:	n/a	n/a
39	POLR2A	chr15:93424807-93429007	IMR90	lung:	n/a	n/a
40	MAFF	chr15:93424242-93425688	K562	blood:	n/a	n/a
41	POLR2A	chr15:93424856-93427475	GM18951	blood:	n/a	n/a
42	POLR2A	chr15:93424885-93425738	GM12891	blood:	n/a	n/a
43	POLR2A	chr15:93424535-93427132	K562	blood:	n/a	n/a
44	POLR2A	chr15:93424802-93427209	GM12892	blood:	n/a	n/a
45	MAX	chr15:93424708-93427418	A549	lung:	n/a	chr15:93426661-93426671
46	RCOR1	chr15:93424516-93426233	K562	blood:	n/a	n/a
47	EP300	chr15:93424455-93426153	K562	blood:	n/a	chr15:93424934-93424948 chr15:93425381-93425391 chr15:93425408-93425422 chr15:93424596-93424603
48	NR2F2	chr15:93424890-93425876	K562	blood:	n/a	n/a
49	SP1	chr15:93424632-93426312	A549	lung:	n/a	chr15:93425998-93426007 chr15:93426000-93426014 chr15:93425704-93425715 chr15:93426006-93426020 chr15:93425701-93425715 chr15:93425997-93426006 chr15:93426003-93426017 chr15:93425996-93426008 chr15:93425730-93425751 chr15:93425618-93425639
50	PML	chr15:93424708-93426281	K562	blood:	n/a	chr15:93426048-93426056

No.	Distal block	Cell Line	Cell type
1	chr15:93385510..93388463-chr15:93423179..93425134,2	K562	blood:
2	chr11:62607333..62609223-chr15:93424710..93426737,2	K562	blood:
3	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
4	chr15:93339450..93342002-chr15:93423524..93425580,2	MCF-7	breast:
5	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
6	chr15:93424784..93426792-chr15:93481094..93482707,2	MCF-7	breast:
7	chr15:93412399..93413366-chr15:93424771..93425883,5	MCF-7	breast:
8	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
9	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
10	chr15:93424876..93427339-chr17:58154118..58156433,2	MCF-7	breast:
11	chr15:93422990..93425055-chr15:93476703..93479164,2	K562	blood:

Variant related genes	Relation type
ENSG00000272888	TF binding region
CHD2	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000068097	Chromatin interaction
ENSG00000258527	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11856160	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2388023	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4778053	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
8	esv3420117	chr15:93423948-93428546	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93412600-93425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:93413600-93425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:93413800-93425200	Weak transcription	Left Ventricle	heart
4	chr15:93420000-93425200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:93420200-93425000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:93420200-93425000	Enhancers	Fetal Heart	heart
7	chr15:93420400-93425200	Weak transcription	Psoas Muscle	Psoas
8	chr15:93421400-93425200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:93421800-93425200	Enhancers	Placenta	Placenta
10	chr15:93421800-93426000	Weak transcription	Ovary	ovary
11	chr15:93422000-93425000	Weak transcription	Lung	lung
12	chr15:93422000-93425200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:93422200-93425000	Weak transcription	Pancreas	Pancrea
14	chr15:93422200-93425200	Weak transcription	Right Ventricle	heart
15	chr15:93422200-93426000	Weak transcription	Gastric	stomach
16	chr15:93423000-93425000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr15:93423200-93425000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:93423200-93425000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr15:93423200-93425000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr15:93423200-93425000	Flanking Active TSS	Thymus	Thymus
21	chr15:93423200-93425200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr15:93423200-93425200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:93423400-93425000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr15:93423400-93425400	Flanking Active TSS	Dnd41	blood
25	chr15:93423400-93425600	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr15:93423600-93425000	Enhancers	Primary B cells from peripheral blood	blood
27	chr15:93423600-93425000	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr15:93423600-93425000	Enhancers	Fetal Brain Male	brain
29	chr15:93423600-93425400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr15:93423600-93425400	Flanking Active TSS	Fetal Thymus	thymus
31	chr15:93423600-93425600	Enhancers	Spleen	Spleen
32	chr15:93423800-93425200	Enhancers	Fetal Intestine Small	intestine
33	chr15:93423800-93425200	Weak transcription	Small Intestine	intestine
34	chr15:93423800-93425400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:93424000-93425000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:93424000-93425000	Enhancers	Hela-S3	cervix
37	chr15:93424000-93425200	Enhancers	Fetal Intestine Large	intestine
38	chr15:93424000-93425400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr15:93424000-93425400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr15:93424000-93425600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:93424000-93425600	Flanking Active TSS	K562	blood
42	chr15:93424200-93425000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:93424200-93425000	Enhancers	NHDF-Ad	bronchial
44	chr15:93424200-93425200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:93424200-93425200	Enhancers	Stomach Mucosa	stomach
46	chr15:93424200-93425400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:93424200-93425400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:93424200-93425400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:93424200-93425400	Flanking Active TSS	A549	lung
50	chr15:93424200-93425400	Flanking Active TSS	NHEK	skin

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