Variant report

Variant	rs963719
Chromosome Location	chr15:93428469-93428470
allele	A/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	GATA3	chr15:93427913-93428742	MCF-7	breast:	n/a	chr15:93428567-93428574 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428567-93428574 chr15:93428566-93428574 chr15:93428562-93428578
2	MAFF	chr15:93427671-93428659	K562	blood:	n/a	n/a
3	POLR2A	chr15:93424491-93428698	GM12891	blood:	n/a	n/a
4	FOXA1	chr15:93428462-93428701	T-47D	breast:	n/a	n/a
5	POLR2A	chr15:93424986-93428747	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:93427558-93429260	U87	brain:	n/a	n/a
7	POLR2A	chr15:93425074-93428806	H1-neurons	neurons:	n/a	n/a
8	REST	chr15:93424836-93430889	H1-neurons	neurons:	n/a	chr15:93425104-93425118
9	REST	chr15:93426327-93428699	A549	lung:	n/a	n/a
10	POLR2A	chr15:93425165-93428729	Hela-S3	cervix:	n/a	n/a
11	EP300	chr15:93427977-93428781	K562	blood:	n/a	chr15:93428724-93428738 chr15:93428420-93428434 chr15:93428337-93428344
12	POLR2A	chr15:93427535-93429280	U87	brain:	n/a	n/a
13	IRF1	chr15:93426917-93428793	K562	blood:	n/a	chr15:93428421-93428435 chr15:93428702-93428714 chr15:93427989-93428001
14	POLR2A	chr15:93424268-93428846	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr15:93427725-93428840	K562	blood:	n/a	chr15:93428047-93428060 chr15:93428047-93428058
16	POLR2A	chr15:93424531-93429178	MCF10A-Er-Src	breast:	n/a	n/a
17	PML	chr15:93427711-93428798	K562	blood:	n/a	n/a
18	CEBPB	chr15:93428440-93428702	A549	lung:	n/a	n/a
19	POLR2A	chr15:93428392-93428750	SK-N-SH	brain:	n/a	n/a
20	YY1	chr15:93427818-93428630	GM12878	blood:	n/a	chr15:93428268-93428278 chr15:93428267-93428279
21	POLR2A	chr15:93426879-93428734	PFSK-1	brain:	n/a	n/a
22	JUND	chr15:93428279-93428854	T-47D	breast:	n/a	n/a
23	ARID3A	chr15:93426945-93428834	K562	blood:	n/a	n/a
24	POLR2A	chr15:93424807-93429007	IMR90	lung:	n/a	n/a
25	POLR2A	chr15:93428367-93428515	Hela-S3	cervix:	n/a	n/a
26	EBF1	chr15:93428451-93428545	GM12878	blood:	n/a	n/a
27	MXI1	chr15:93427942-93428832	GM12878	blood:	n/a	n/a
28	FOS	chr15:93428458-93428834	MCF10A-Er-Src	breast:	n/a	n/a
29	REST	chr15:93428382-93429172	H1-neurons	neurons:	n/a	n/a
30	GATA3	chr15:93427897-93428812	T-47D	breast:	n/a	chr15:93428567-93428574 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428567-93428574 chr15:93428566-93428574 chr15:93428562-93428578
31	GATA3	chr15:93428368-93428734	T-47D	breast:	n/a	chr15:93428567-93428574 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428567-93428574 chr15:93428566-93428574 chr15:93428562-93428578
32	YY1	chr15:93427085-93428489	SK-N-SH	brain:	n/a	chr15:93428268-93428278 chr15:93428267-93428279
33	CUX1	chr15:93428205-93428681	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:93428122-93428698	K562	blood:	n/a	n/a
35	POLR2A	chr15:93424455-93428727	PBDE	blood:	n/a	n/a
36	GATA3	chr15:93427855-93428862	SK-N-SH	brain:	n/a	chr15:93428567-93428574 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428567-93428574 chr15:93428566-93428574 chr15:93428562-93428578
37	FOXA1	chr15:93428420-93428855	T-47D	breast:	n/a	n/a
38	POLR2A	chr15:93424634-93429306	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr15:93426367-93428667	PANC-1	pancreas:	n/a	n/a
40	GATA3	chr15:93427702-93428879	SK-N-SH	brain:	n/a	chr15:93428567-93428574 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428567-93428574 chr15:93428566-93428574 chr15:93428562-93428578
41	POLR2A	chr15:93427505-93431721	HepG2	liver:	n/a	n/a
42	TBP	chr15:93428191-93428718	Hela-S3	cervix:	n/a	n/a
43	MXI1	chr15:93423850-93428882	SK-N-SH	brain:	n/a	chr15:93425142-93425157
44	CHD1	chr15:93424901-93431299	IMR90	lung:	n/a	chr15:93426483-93426493 chr15:93426003-93426013
45	POLR2A	chr15:93425895-93428730	GM12878	blood:	n/a	n/a
46	STAT3	chr15:93426824-93428729	Hela-S3	cervix:	n/a	chr15:93427132-93427139
47	GATA2	chr15:93428397-93428731	HUVEC	blood vessel:	n/a	chr15:93428567-93428574 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428564-93428578 chr15:93428567-93428574 chr15:93428562-93428578
48	GATA3	chr15:93427691-93428756	SH-SY5Y	brain:	n/a	chr15:93428567-93428574 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428567-93428574 chr15:93428566-93428574 chr15:93428562-93428578
49	CHD1	chr15:93425092-93429680	GM12878	blood:	n/a	chr15:93426483-93426493 chr15:93426003-93426013
50	GATA3	chr15:93425083-93428893	A549	lung:	n/a	chr15:93428567-93428574 chr15:93428863-93428884 chr15:93428567-93428574 chr15:93428567-93428577 chr15:93428560-93428581 chr15:93428567-93428574 chr15:93428566-93428574 chr15:93428562-93428578

No.	Distal block	Cell Line	Cell type
1	chr15:93181102..93183442-chr15:93428358..93430400,2	MCF-7	breast:
2	chr15:93352456..93353356-chr15:93428226..93429092,2	MCF-7	breast:
3	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
4	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
5	chr15:93352604..93353121-chr15:93427828..93428651,2	Hela-S3	cervix:
6	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
7	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
8	chr15:93197537..93199243-chr15:93427702..93429402,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD2-6	chr15:93427601-93428814	ENSG00000272888.1

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16947279	1.00[AMR][1000 genomes]
rs1898914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1898915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2272454	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2272455	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2272456	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2388053	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs41439544	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4778071	1.00[AFR][1000 genomes]
rs57518365	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs57602473	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs58304402	1.00[AFR][1000 genomes]
rs58367771	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs58592069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60297312	1.00[ASN][1000 genomes]
rs60635695	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61017356	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61035863	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61286161	1.00[AFR][1000 genomes]
rs61334597	1.00[AFR][1000 genomes];0.80[AMR][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93424400-93430800	Active TSS	Aorta	Aorta
2	chr15:93424600-93429200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:93424800-93428600	Active TSS	Colonic Mucosa	Colon
4	chr15:93424800-93429400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr15:93425000-93428800	Active TSS	Thymus	Thymus
6	chr15:93425000-93429200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:93425000-93429200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:93425000-93429200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:93425000-93431800	Active TSS	Right Atrium	heart
10	chr15:93425200-93428800	Active TSS	Psoas Muscle	Psoas
11	chr15:93425200-93428800	Active TSS	Right Ventricle	heart
12	chr15:93425200-93429000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:93425400-93428800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr15:93425400-93428800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr15:93425400-93428800	Active TSS	Brain Cingulate Gyrus	brain
16	chr15:93425400-93428800	Active TSS	Brain Substantia Nigra	brain
17	chr15:93425400-93429000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr15:93425400-93429000	Active TSS	Brain Angular Gyrus	brain
19	chr15:93425400-93429000	Active TSS	Fetal Intestine Large	intestine
20	chr15:93425400-93429000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr15:93425400-93429000	Active TSS	Rectal Smooth Muscle	rectum
22	chr15:93425400-93429200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr15:93425400-93429200	Active TSS	A549	lung
24	chr15:93425400-93429400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:93425400-93429400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:93425400-93429400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:93425400-93429400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:93425400-93429400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:93425400-93429400	Active TSS	Brain Anterior Caudate	brain
30	chr15:93425400-93429400	Active TSS	Duodenum Mucosa	Duodenum
31	chr15:93425400-93429400	Active TSS	Fetal Kidney	kidney
32	chr15:93425400-93429400	Active TSS	Fetal Thymus	thymus
33	chr15:93425400-93429400	Active TSS	NHEK	skin
34	chr15:93425400-93429600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr15:93425400-93429600	Active TSS	Colon Smooth Muscle	Colon
36	chr15:93425400-93429600	Active TSS	NHLF	lung
37	chr15:93425400-93430000	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr15:93425400-93430000	Active TSS	Brain Hippocampus Middle	brain
39	chr15:93425400-93430000	Active TSS	HSMMtube	muscle
40	chr15:93425400-93430400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:93425400-93430800	Active TSS	Stomach Smooth Muscle	stomach
42	chr15:93425600-93428600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr15:93425600-93428600	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr15:93425600-93428600	Active TSS	Primary B cells from peripheral blood	blood
45	chr15:93425600-93428600	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr15:93425600-93428600	Active TSS	NH-A	brain
47	chr15:93425600-93428800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr15:93425600-93428800	Active TSS	Fetal Intestine Small	intestine
49	chr15:93425600-93428800	Active TSS	Fetal Muscle Trunk	muscle
50	chr15:93425600-93428800	Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links