Variant report

Variant	rs16945247
Chromosome Location	chr17:59492087-59492088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr17:59491679-59492174	HepG2	liver:	n/a	n/a
2	GATA3	chr17:59491635-59494906	MCF-7	breast:	n/a	chr17:59491884-59491894 chr17:59492575-59492585
3	TEAD4	chr17:59484276-59495088	A549	lung:	n/a	n/a
4	POLR2A	chr17:59491743-59492126	HepG2	liver:	n/a	n/a
5	MYC	chr17:59492083-59492112	HepG2	liver:	n/a	n/a
6	MAX	chr17:59484138-59500997	MCF-7	breast:	n/a	chr17:59495541-59495552 chr17:59492978-59492987 chr17:59491213-59491223 chr17:59491485-59491495 chr17:59495570-59495581 chr17:59488910-59488926
7	POLR2A	chr17:59491511-59492389	ProgFib	skin:	n/a	n/a
8	SMC3	chr17:59485817-59492815	SK-N-SH	brain:	n/a	chr17:59488339-59488353 chr17:59491210-59491220 chr17:59488343-59488353
9	RAD21	chr17:59491533-59495532	SK-N-SH	brain:	n/a	chr17:59494032-59494042 chr17:59494302-59494312 chr17:59494404-59494413
10	ZNF274	chr17:59491519-59492153	GM08714	blood:	n/a	n/a
11	HDAC2	chr17:59482687-59495676	MCF-7	breast:	n/a	chr17:59487075-59487094 chr17:59495598-59495612 chr17:59495596-59495610 chr17:59495599-59495613 chr17:59495595-59495609 chr17:59494256-59494265 chr17:59492574-59492588
12	MYBL2	chr17:59491682-59492126	HepG2	liver:	n/a	n/a
13	HDAC2	chr17:59491726-59492138	HepG2	liver:	n/a	n/a

No data

(count:39 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59489649..59492493-chr3:119811877..119814556,2	MCF-7	breast:
2	chr17:57079759..57081712-chr17:59490275..59492386,2	MCF-7	breast:
3	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
4	chr17:59483268..59486484-chr17:59491273..59493392,3	K562	blood:
5	chr17:59491921..59492760-chr20:49343640..49344491,3	MCF-7	breast:
6	chr17:57916842..57918701-chr17:59490390..59492467,2	MCF-7	breast:
7	chr17:59492061..59493575-chr2:55052880..55054380,2	MCF-7	breast:
8	chr17:59491164..59492814-chr20:52697819..52700709,2	MCF-7	breast:
9	chr17:59491684..59493481-chr7:20368667..20370695,2	MCF-7	breast:
10	chr17:59094691..59097620-chr17:59491568..59493093,2	MCF-7	breast:
11	chr17:59490811..59493565-chr9:80089592..80091840,2	MCF-7	breast:
12	chr17:59490397..59493114-chr17:60868555..60870113,2	MCF-7	breast:
13	chr17:59490690..59492764-chr20:52480509..52482719,2	MCF-7	breast:
14	chr17:59491612..59493319-chr17:59927400..59929944,2	MCF-7	breast:
15	chr17:59486789..59493376-chr20:46130669..46135131,5	MCF-7	breast:
16	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
17	chr17:59489843..59492538-chr20:52557995..52559827,2	MCF-7	breast:
18	chr17:59490768..59492795-chr20:42086265..42087870,2	MCF-7	breast:
19	chr17:59489837..59492539-chr20:52768488..52770171,2	MCF-7	breast:
20	chr17:59490269..59492891-chr17:73768082..73769932,2	MCF-7	breast:
21	chr17:59489238..59492668-chr17:59650942..59653805,58	MCF-7	breast:
22	chr17:59489427..59492418-chr17:59944294..59946744,2	MCF-7	breast:
23	chr17:59491901..59492565-chr17:59800428..59800934,2	MCF-7	breast:
24	chr17:59085731..59087853-chr17:59489578..59492424,2	MCF-7	breast:
25	chr17:59491548..59493731-chr17:64460964..64463383,2	MCF-7	breast:
26	chr17:59490904..59493858-chr5:81572794..81575325,2	MCF-7	breast:
27	chr17:59486918..59494123-chr20:45984608..45990861,17	MCF-7	breast:
28	chr17:59491669..59494227-chr20:52486642..52489549,2	MCF-7	breast:
29	chr17:59490326..59492586-chr17:59938992..59941381,2	MCF-7	breast:
30	chr17:59486255..59492170-chr17:59932286..59941695,13	MCF-7	breast:
31	chr17:59491155..59493434-chr3:64672960..64675893,2	MCF-7	breast:
32	chr17:59491624..59492156-chr17:59660433..59661053,2	MCF-7	breast:
33	chr17:57968948..57972099-chr17:59491363..59493598,3	MCF-7	breast:
34	chr17:59489687..59492860-chr20:52555075..52557067,4	MCF-7	breast:
35	chr17:56735008..56738004-chr17:59488690..59493037,7	MCF-7	breast:
36	chr17:59489914..59492282-chr20:55683243..55685031,2	MCF-7	breast:
37	chr17:57913418..57928047-chr17:59480816..59492160,26	MCF-7	breast:
38	chr17:59489853..59492100-chr20:52604807..52606862,2	MCF-7	breast:
39	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267280	TF binding region
ENSG00000236352	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000186468	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000082701	Chromatin interaction
ENSG00000108443	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000242622	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000163638	Chromatin interaction
ENSG00000205464	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000124193	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000105855	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28696765	1.00[AMR][1000 genomes]
rs9898324	0.92[ASW][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9905879	1.00[AMR][1000 genomes]
rs9913766	1.00[AMR][1000 genomes]
rs9915629	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
5	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
6	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
7	nsv908668	chr17:59471151-59494574	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	263 gene(s)	inside rSNPs	diseases
8	nsv908670	chr17:59471372-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	262 gene(s)	inside rSNPs	diseases
9	nsv908671	chr17:59475888-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
10	nsv908672	chr17:59476062-59494574	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
11	nsv519931	chr17:59491281-59514461	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59490200-59493800	Weak transcription	K562	blood
2	chr17:59490400-59493600	Weak transcription	HSMMtube	muscle
3	chr17:59490400-59493800	Weak transcription	Liver	Liver
4	chr17:59490600-59493800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr17:59490600-59493800	Weak transcription	Brain Angular Gyrus	brain
6	chr17:59490600-59493800	Weak transcription	Gastric	stomach
7	chr17:59490600-59494000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:59490600-59494000	Weak transcription	Esophagus	oesophagus
9	chr17:59490600-59494000	Weak transcription	HMEC	breast
10	chr17:59490600-59494200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr17:59490600-59494200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr17:59490800-59492600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr17:59490800-59493200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:59490800-59494000	Weak transcription	Brain Anterior Caudate	brain
15	chr17:59490800-59494000	Weak transcription	Brain Substantia Nigra	brain
16	chr17:59490800-59494000	Weak transcription	Pancreas	Pancrea
17	chr17:59491000-59492200	Enhancers	Right Atrium	heart
18	chr17:59491000-59492400	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr17:59491000-59492400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr17:59491000-59493200	Weak transcription	NH-A	brain
21	chr17:59491000-59493600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:59491000-59493800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:59491000-59493800	Enhancers	Adipose Nuclei	Adipose
24	chr17:59491000-59493800	Weak transcription	Fetal Heart	heart
25	chr17:59491000-59493800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr17:59491000-59493800	Enhancers	NHDF-Ad	bronchial
27	chr17:59491000-59494000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:59491000-59494000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr17:59491000-59494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:59491000-59494000	Bivalent Enhancer	Fetal Stomach	stomach
31	chr17:59491000-59494600	Enhancers	Lung	lung
32	chr17:59491000-59495600	Enhancers	Placenta	Placenta
33	chr17:59491000-59504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:59491200-59492200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:59491200-59492600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr17:59491200-59493800	Enhancers	Osteobl	bone
37	chr17:59491200-59494000	Weak transcription	Fetal Kidney	kidney
38	chr17:59491400-59492200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:59491400-59492200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:59491400-59493200	Enhancers	Spleen	Spleen
41	chr17:59491600-59492200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:59491600-59492200	Enhancers	Left Ventricle	heart
43	chr17:59491600-59492400	Enhancers	Right Ventricle	heart
44	chr17:59491600-59492400	Flanking Active TSS	HepG2	liver
45	chr17:59491600-59492800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr17:59491800-59492200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr17:59491800-59492200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:59491800-59492200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr17:59491800-59494600	Enhancers	NHLF	lung
50	chr17:59492000-59492400	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links