Variant report

Variant	rs2917669
Chromosome Location	chr16:69759220-69759221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:69757538-69761443	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:69758933-69759511	HepG2	liver:	n/a	n/a
3	FOXA2	chr16:69758952-69759393	HepG2	liver:	n/a	n/a
4	FOS	chr16:69759167-69759333	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr16:69758784-69762098	Hela-S3	cervix:	n/a	n/a
6	MAX	chr16:69758996-69759502	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr16:69759144-69759512	K562	blood:	n/a	chr16:69759456-69759467
8	HA-E2F1	chr16:69759113-69761041	MCF-7	breast:	n/a	chr16:69760366-69760375
9	POLR2A	chr16:69759024-69762149	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr16:69759014-69759559	K562	blood:	n/a	n/a
11	HEY1	chr16:69758796-69761112	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:69759196-69759511	MCF10A-Er-Src	breast:	n/a	n/a
13	HEY1	chr16:69758446-69761187	HepG2	liver:	n/a	n/a
14	TEAD4	chr16:69758753-69759409	HepG2	liver:	n/a	n/a
15	TBL1XR1	chr16:69759091-69759513	K562	blood:	n/a	n/a
16	ZMIZ1	chr16:69758814-69759340	K562	blood:	n/a	n/a
17	ETS1	chr16:69759104-69759626	A549	lung:	n/a	n/a
18	HDAC2	chr16:69758909-69759503	K562	blood:	n/a	n/a
19	FOXA1	chr16:69758874-69759352	HepG2	liver:	n/a	n/a
20	POLR2A	chr16:69758775-69759491	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr16:69759018-69759249	ECC-1	luminal epithelium:	n/a	n/a
22	NR2F2	chr16:69759127-69759694	K562	blood:	n/a	chr16:69759354-69759369
23	RCOR1	chr16:69759194-69761174	Hela-S3	cervix:	n/a	n/a
24	NR2F2	chr16:69759143-69761441	K562	blood:	n/a	chr16:69759354-69759369
25	POLR2A	chr16:69758492-69759584	HepG2	liver:	n/a	n/a
26	MXI1	chr16:69759085-69759324	K562	blood:	n/a	n/a
27	EP300	chr16:69759068-69759303	K562	blood:	n/a	n/a
28	HDAC2	chr16:69759007-69759712	K562	blood:	n/a	n/a
29	BHLHE40	chr16:69759187-69759673	K562	blood:	n/a	n/a
30	POLR2A	chr16:69758539-69761198	HepG2	liver:	n/a	n/a
31	TBP	chr16:69758734-69759541	HepG2	liver:	n/a	n/a
32	TCF12	chr16:69758736-69761990	A549	lung:	n/a	n/a
33	POLR2A	chr16:69758931-69761864	MCF-7	breast:	n/a	n/a
34	CEBPB	chr16:69759092-69759460	HepG2	liver:	n/a	n/a
35	MYBL2	chr16:69758711-69759756	HepG2	liver:	n/a	n/a
36	CEBPB	chr16:69759074-69759509	A549	lung:	n/a	chr16:69759456-69759467
37	ZC3H11A	chr16:69759073-69759288	K562	blood:	n/a	n/a
38	RCOR1	chr16:69758848-69761598	K562	blood:	n/a	n/a
39	POLR2A	chr16:69758874-69759555	HepG2	liver:	n/a	n/a
40	MBD4	chr16:69758545-69759574	HepG2	liver:	n/a	n/a
41	POLR2A	chr16:69758605-69759650	A549	lung:	n/a	n/a
42	POLR2A	chr16:69758963-69761404	HCT-116	colon:	n/a	n/a
43	STAT3	chr16:69759178-69759276	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr16:69758793-69759595	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr16:69758886-69761355	MCF-7	breast:	n/a	n/a
46	MYBL2	chr16:69758309-69761134	HepG2	liver:	n/a	n/a
47	TBP	chr16:69759208-69761606	K562	blood:	n/a	n/a
48	CEBPB	chr16:69759058-69759424	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr16:69758615-69759511	HepG2	liver:	n/a	n/a
50	POLR2A	chr16:69758967-69761334	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69755811..69761889-chr16:69791851..69798633,14	K562	blood:
2	chr16:69599623..69601716-chr16:69757663..69760565,3	MCF-7	breast:
3	chr16:69758127..69765240-chr16:69786072..69790209,13	K562	blood:
4	chr16:69741703..69743553-chr16:69758543..69761964,3	MCF-7	breast:
5	chr16:69363088..69367214-chr16:69757729..69760450,3	MCF-7	breast:
6	chr16:69757296..69762552-chr16:69785671..69789636,11	K562	blood:
7	chr16:69757781..69759922-chr16:69795313..69797984,2	MCF-7	breast:
8	chr16:69756628..69762611-chr16:69781362..69792848,24	MCF-7	breast:
9	chr16:69757858..69760516-chr16:69796168..69797980,2	MCF-7	breast:
10	chr16:69759185..69761889-chr16:69795379..69799385,4	K562	blood:
11	chr16:69757413..69759296-chr16:69767966..69769499,2	K562	blood:
12	chr16:69758592..69760994-chr16:70729394..70731021,2	K562	blood:
13	chr16:69741680..69751385-chr16:69755023..69763559,18	MCF-7	breast:
14	chr16:69759014..69761546-chr17:57916568..57918656,2	MCF-7	breast:
15	chr16:69756730..69759339-chr16:69925366..69928011,2	K562	blood:
16	chr15:75931960..75934199-chr16:69758900..69760428,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000262136	TF binding region
ENSG00000177971	Chromatin interaction
ENSG00000261602	Chromatin interaction
ENSG00000260290	Chromatin interaction
ENSG00000198373	Chromatin interaction
ENSG00000238683	Chromatin interaction
ENSG00000102908	Chromatin interaction
ENSG00000103043	Chromatin interaction
ENSG00000258429	Chromatin interaction
ENSG00000223109	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000141101	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10517	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10852459	0.82[CHB][hapmap]
rs11075736	0.89[EUR][1000 genomes]
rs1139177	0.82[EUR][1000 genomes]
rs1142105	0.89[ASN][1000 genomes]
rs11862697	1.00[CEU][hapmap]
rs12019048	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs12102305	0.83[ASN][1000 genomes]
rs12921017	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1318651	1.00[CEU][hapmap]
rs13329844	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs13331055	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13331071	0.84[ASN][1000 genomes]
rs13331216	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13335149	0.87[ASN][1000 genomes]
rs13335664	0.88[ASN][1000 genomes]
rs13338560	0.80[AMR][1000 genomes]
rs16958965	0.84[ASN][1000 genomes]
rs16958997	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs16959059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16959266	1.00[CEU][hapmap]
rs2088747	1.00[CEU][hapmap]
rs2291960	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs2304526	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs28392989	0.85[ASN][1000 genomes]
rs28473508	0.82[ASN][1000 genomes]
rs2917665	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2917667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2917672	0.90[ASN][1000 genomes]
rs2917673	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917675	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2917676	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917681	0.88[CEU][hapmap]
rs2917682	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2917683	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2937125	0.82[CHB][hapmap]
rs2937126	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs2965752	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2965753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs2965757	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs2965759	1.00[CEU][hapmap]
rs3785075	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs3790084	0.87[CEU][hapmap]
rs3790087	1.00[CEU][hapmap]
rs3790088	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs3826153	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs3826154	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3926183	0.82[ASN][1000 genomes]
rs4247107	0.82[EUR][1000 genomes]
rs4247109	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs4442796	0.88[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap]
rs4985527	1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[TSI][hapmap]
rs4985547	0.82[CHB][hapmap]
rs61628167	0.84[ASN][1000 genomes]
rs6499246	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499248	0.82[EUR][1000 genomes]
rs6499249	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs6499259	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs689452	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689456	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200270	0.81[ASN][1000 genomes]
rs7200420	0.93[ASN][1000 genomes]
rs7204615	0.85[EUR][1000 genomes]
rs7359387	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs8057938	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9888980	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs9888981	1.00[CEU][hapmap]
rs9888993	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs9889219	0.81[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9921652	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs9922223	1.00[CEU][hapmap]
rs9924264	0.85[ASN][1000 genomes]
rs9924271	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs9924953	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs9925037	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs9927809	0.92[ASN][1000 genomes]
rs9932486	1.00[CEU][hapmap]
rs9934264	0.87[ASN][1000 genomes]
rs9934321	0.92[ASN][1000 genomes]
rs9934681	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9936464	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs9937018	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9940008	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv517207	chr16:69745145-69771914	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2917669	FUK	cis	parietal	SCAN
rs2917669	GFOD2	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
2	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
3	chr16:69729400-69760000	Weak transcription	Ovary	ovary
4	chr16:69730600-69759800	Weak transcription	Fetal Brain Female	brain
5	chr16:69730800-69759800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr16:69731800-69759600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr16:69731800-69759800	Weak transcription	Primary B cells from cord blood	blood
8	chr16:69731800-69759800	Weak transcription	Right Ventricle	heart
9	chr16:69733800-69759800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr16:69738800-69759800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr16:69739200-69759800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr16:69741000-69759400	Weak transcription	Small Intestine	intestine
13	chr16:69741600-69759800	Weak transcription	Primary T cells from cord blood	blood
14	chr16:69743800-69760000	Weak transcription	Fetal Kidney	kidney
15	chr16:69744000-69759800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr16:69745400-69759800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr16:69747200-69759600	Weak transcription	Thymus	Thymus
18	chr16:69747400-69759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:69747400-69759800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr16:69747400-69759800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr16:69749400-69759800	Weak transcription	Brain Angular Gyrus	brain
22	chr16:69749400-69760000	Weak transcription	Fetal Lung	lung
23	chr16:69749600-69760000	Weak transcription	Pancreas	Pancrea
24	chr16:69749800-69759800	Weak transcription	Colon Smooth Muscle	Colon
25	chr16:69751400-69759400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr16:69751600-69760000	Weak transcription	Liver	Liver
27	chr16:69752400-69759400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr16:69752400-69759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr16:69752400-69759800	Weak transcription	Esophagus	oesophagus
30	chr16:69752400-69760000	Weak transcription	Aorta	Aorta
31	chr16:69752600-69759800	Weak transcription	Left Ventricle	heart
32	chr16:69752600-69760000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr16:69754800-69759600	Transcr. at gene 5' and 3'	A549	lung
34	chr16:69755400-69759400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr16:69756200-69759800	Enhancers	Fetal Intestine Small	intestine
36	chr16:69756400-69759400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr16:69756800-69759600	Flanking Active TSS	HepG2	liver
38	chr16:69756800-69760600	Active TSS	Stomach Mucosa	stomach
39	chr16:69757600-69759400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr16:69757800-69759400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
41	chr16:69757800-69759600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr16:69758200-69761200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr16:69758400-69759400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:69758400-69759600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr16:69758400-69759600	Flanking Active TSS	Hela-S3	cervix
46	chr16:69758400-69759800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr16:69758600-69759400	Weak transcription	Lung	lung
48	chr16:69758600-69759600	Flanking Active TSS	GM12878-XiMat	blood
49	chr16:69758600-69759600	Flanking Active TSS	HMEC	breast
50	chr16:69758600-69759600	Flanking Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links