Variant report

Variant	rs16969507
Chromosome Location	chr15:78405617-78405618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:125)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:125 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:78405491-78405872	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr15:78405600-78405824	MCF-7	breast:	n/a	n/a
3	RAD21	chr15:78405512-78405949	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr15:78405552-78405848	T-47D	breast:	n/a	n/a
5	CTCF	chr15:78405609-78405830	ProgFib	skin:	n/a	n/a
6	CTCF	chr15:78405608-78405863	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr15:78405604-78405860	Kidney_OC	kidney:	n/a	n/a
8	CTCF	chr15:78405549-78405841	A549	lung:	n/a	n/a
9	CTCF	chr15:78405532-78405843	GM10248	blood:	n/a	n/a
10	RAD21	chr15:78405503-78405905	HepG2	liver:	n/a	n/a
11	RAD21	chr15:78405304-78406065	A549	lung:	n/a	n/a
12	CTCF	chr15:78405590-78405845	GM13976	blood:	n/a	n/a
13	RELA	chr15:78405410-78405876	GM18951	blood:	n/a	chr15:78405663-78405672 chr15:78405663-78405672
14	TBL1XR1	chr15:78405541-78405857	GM12878	blood:	n/a	n/a
15	FOXM1	chr15:78405499-78405901	GM12878	blood:	n/a	n/a
16	CTCF	chr15:78405598-78405883	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr15:78405605-78405844	NHEK	skin:	n/a	n/a
18	CTCF	chr15:78405494-78405962	IMR90	lung:	n/a	n/a
19	BCL3	chr15:78405280-78405950	A549	lung:	n/a	chr15:78405662-78405671
20	IRF1	chr15:78405519-78405871	K562	blood:	n/a	n/a
21	TCF12	chr15:78405253-78406015	A549	lung:	n/a	n/a
22	CTCF	chr15:78405505-78405950	GM12878	blood:	n/a	n/a
23	TEAD4	chr15:78405507-78405810	H1-hESC	embryonic stem cell:	n/a	chr15:78405599-78405608
24	EBF1	chr15:78405569-78405847	GM12878	blood:	n/a	n/a
25	CTCF	chr15:78405431-78405918	A549	lung:	n/a	n/a
26	SMC3	chr15:78405480-78405940	HepG2	liver:	n/a	n/a
27	CTCF	chr15:78405600-78405750	HAc	cerebellar:	n/a	n/a
28	SMC3	chr15:78405370-78405939	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr15:78405234-78405952	SK-N-SH	brain:	n/a	n/a
30	YY1	chr15:78405528-78405834	GM12878	blood:	n/a	n/a
31	CTCF	chr15:78405565-78405843	GM19240	blood:	n/a	n/a
32	RELA	chr15:78405482-78405921	GM19099	blood:	n/a	chr15:78405663-78405672 chr15:78405663-78405672
33	MAZ	chr15:78405594-78405848	K562	blood:	n/a	n/a
34	RAD21	chr15:78405505-78405919	A549	lung:	n/a	n/a
35	CTCF	chr15:78405580-78405730	A549	lung:	n/a	n/a
36	CTCF	chr15:78405476-78405841	H1-hESC	embryonic stem cell:	n/a	n/a
37	RUNX3	chr15:78405491-78405927	GM12878	blood:	n/a	n/a
38	CTCF	chr15:78405520-78405670	GM12865	blood:	n/a	n/a
39	RAD21	chr15:78405564-78405879	GM12878	blood:	n/a	n/a
40	RAD21	chr15:78405449-78405885	HCT-116	colon:	n/a	n/a
41	ELK1	chr15:78405604-78405855	GM12878	blood:	n/a	n/a
42	CTCF	chr15:78405465-78405887	MCF-7	breast:	n/a	n/a
43	FOXM1	chr15:78405408-78406066	GM12878	blood:	n/a	n/a
44	RUNX3	chr15:78405566-78405835	GM12878	blood:	n/a	n/a
45	RAD21	chr15:78405411-78406004	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr15:78405533-78405906	HepG2	liver:	n/a	n/a
47	CTCF	chr15:78405181-78405956	SK-N-SH	brain:	n/a	n/a
48	RAD21	chr15:78405544-78405960	HepG2	liver:	n/a	n/a
49	RAD21	chr15:78405510-78405937	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr15:78405546-78405844	GM19238	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78405195..78406276-chr15:78487287..78488630,12	K562	blood:
2	chr15:78405315..78406539-chr15:78533006..78535187,14	MCF-7	breast:
3	chr15:78404966..78407239-chr15:78487303..78489850,2	MCF-7	breast:
4	chr15:78405253..78406238-chr15:78532986..78534064,5	K562	blood:
5	chr15:78279643..78281604-chr15:78403456..78405899,2	K562	blood:
6	chr15:78403982..78406410-chr15:78531457..78533698,3	MCF-7	breast:
7	chr15:78405277..78406290-chr15:78487151..78488696,13	MCF-7	breast:
8	chr15:78234203..78236123-chr15:78404295..78405795,2	MCF-7	breast:
9	chr15:78404287..78406239-chr15:78590590..78593267,2	MCF-7	breast:
10	chr15:78405471..78408380-chr15:78587851..78589863,2	MCF-7	breast:

No data

Variant related genes	Relation type
CIB2	TF binding region
ENSG00000140395	Chromatin interaction
ENSG00000214646	Chromatin interaction
ENSG00000261143	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11072728	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs11072729	0.93[CHB][hapmap];0.86[CHD][hapmap]
rs11639461	0.95[ASN][1000 genomes]
rs12442037	1.00[CEU][hapmap]
rs1542100	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969514	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs16969548	1.00[CEU][hapmap]
rs1971151	0.92[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2271901	1.00[CEU][hapmap]
rs2304823	1.00[CEU][hapmap]
rs2304827	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304829	0.81[ASN][1000 genomes]
rs2867922	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3784328	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784330	0.91[ASN][1000 genomes]
rs60121404	0.93[AMR][1000 genomes]
rs62009267	0.95[ASN][1000 genomes]
rs7161765	0.92[ASN][1000 genomes]
rs7164338	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs72732564	0.95[ASN][1000 genomes]
rs7359294	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032449	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs8036417	0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78393200-78406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78396200-78421800	Weak transcription	Right Ventricle	heart
3	chr15:78396600-78423800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:78397600-78421400	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:78398400-78423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:78398600-78413200	Weak transcription	Spleen	Spleen
7	chr15:78398800-78406200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:78400000-78412800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:78400000-78422400	Weak transcription	Brain Germinal Matrix	brain
10	chr15:78400200-78414600	Weak transcription	Fetal Brain Female	brain
11	chr15:78401400-78413000	Weak transcription	Fetal Stomach	stomach
12	chr15:78401400-78414400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:78402600-78406200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:78403800-78412200	Weak transcription	Thymus	Thymus
15	chr15:78405400-78406000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:78405400-78406000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:78405400-78406000	Genic enhancers	Fetal Intestine Small	intestine
18	chr15:78405400-78406000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:78405400-78406000	Active TSS	A549	lung
20	chr15:78405400-78406400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:78405400-78406400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr15:78405400-78406400	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:78405600-78405800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:78405600-78405800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:78405600-78405800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:78405600-78405800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr15:78405600-78406000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:78405600-78406000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:78405600-78406000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:78405600-78406000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:78405600-78406000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr15:78405600-78406000	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr15:78405600-78406000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr15:78405600-78406000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr15:78405600-78406000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr15:78405600-78406000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr15:78405600-78406000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:78405600-78406000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr15:78405600-78406000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:78405600-78406000	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr15:78405600-78406000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:78405600-78406000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:78405600-78406000	Active TSS	Brain Angular Gyrus	brain
44	chr15:78405600-78406000	Active TSS	Brain Anterior Caudate	brain
45	chr15:78405600-78406000	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr15:78405600-78406000	Active TSS	Fetal Intestine Large	intestine
47	chr15:78405600-78406000	Active TSS	Fetal Kidney	kidney
48	chr15:78405600-78406000	Flanking Active TSS	Fetal Thymus	thymus
49	chr15:78405600-78406000	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr15:78405600-78406000	Active TSS	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links