Variant report

Variant	rs4459608
Chromosome Location	chr17:59491030-59491031
allele	A/C
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	MAX	chr17:59489260-59491073	HepG2	liver:	n/a	n/a
2	GATA2	chr17:59490632-59491192	SH-SY5Y	brain:	n/a	n/a
3	RAD21	chr17:59487656-59491474	SK-N-SH	brain:	n/a	chr17:59488343-59488353 chr17:59488338-59488357 chr17:59491210-59491220 chr17:59488536-59488550 chr17:59488875-59488884 chr17:59488341-59488354 chr17:59487989-59487999 chr17:59488343-59488355
4	TEAD4	chr17:59484276-59495088	A549	lung:	n/a	n/a
5	CTCF	chr17:59487481-59491170	SK-N-SH	brain:	n/a	chr17:59488340-59488353 chr17:59488339-59488360 chr17:59488875-59488883 chr17:59488337-59488355 chr17:59488587-59488600 chr17:59488868-59488886 chr17:59488590-59488603 chr17:59488342-59488352 chr17:59488534-59488547
6	RAD21	chr17:59483140-59491480	MCF-7	breast:	n/a	chr17:59488343-59488353 chr17:59488338-59488357 chr17:59491210-59491220 chr17:59488536-59488550 chr17:59488875-59488884 chr17:59488341-59488354 chr17:59487989-59487999 chr17:59488343-59488355
7	GATA3	chr17:59488556-59491169	MCF-7	breast:	n/a	chr17:59489068-59489078
8	GATA3	chr17:59490833-59491157	SH-SY5Y	brain:	n/a	n/a
9	POLR2A	chr17:59486113-59491295	IMR90	lung:	n/a	n/a
10	MBD4	chr17:59490267-59491152	HepG2	liver:	n/a	n/a
11	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
12	POLR2A	chr17:59485546-59491030	SK-N-SH	brain:	n/a	n/a
13	SMC3	chr17:59485817-59492815	SK-N-SH	brain:	n/a	chr17:59488339-59488353 chr17:59491210-59491220 chr17:59488343-59488353
14	POLR2A	chr17:59489820-59491098	HepG2	liver:	n/a	n/a
15	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

No.	Distal block	Cell Line	Cell type
1	chr17:59487822..59491370-chr20:49345755..49351152,8	MCF-7	breast:
2	chr17:59489649..59492493-chr3:119811877..119814556,2	MCF-7	breast:
3	chr17:57079759..57081712-chr17:59490275..59492386,2	MCF-7	breast:
4	chr17:59488630..59491909-chr20:52682988..52685576,3	MCF-7	breast:
5	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
6	chr17:59488147..59491206-chr17:73773645..73776030,4	MCF-7	breast:
7	chr17:59488387..59491331-chr17:73367342..73369969,2	MCF-7	breast:
8	chr17:59489293..59491949-chr8:125051873..125054864,2	MCF-7	breast:
9	chr17:59489613..59491206-chr17:59800419..59803266,2	MCF-7	breast:
10	chr17:57916842..57918701-chr17:59490390..59492467,2	MCF-7	breast:
11	chr17:59489912..59492013-chr20:52685644..52687540,2	MCF-7	breast:
12	chr17:59490811..59493565-chr9:80089592..80091840,2	MCF-7	breast:
13	chr17:59489184..59491261-chr17:59650345..59653673,119	MCF-7	breast:
14	chr17:59489445..59491262-chr17:59628200..59629244,34	MCF-7	breast:
15	chr17:59488984..59491525-chr17:73774194..73776083,3	MCF-7	breast:
16	chr17:59489384..59491650-chr6:42749691..42752599,2	MCF-7	breast:
17	chr17:59490397..59493114-chr17:60868555..60870113,2	MCF-7	breast:
18	chr17:59490690..59492764-chr20:52480509..52482719,2	MCF-7	breast:
19	chr17:59488570..59491510-chr6:31618990..31620979,2	MCF-7	breast:
20	chr17:59489097..59491505-chr20:52824203..52825940,2	MCF-7	breast:
21	chr17:59486789..59493376-chr20:46130669..46135131,5	MCF-7	breast:
22	chr17:59489225..59491342-chr17:73769759..73771486,2	MCF-7	breast:
23	chr17:59488402..59491332-chr5:170814071..170816184,2	MCF-7	breast:
24	chr1:78017249..78019893-chr17:59489545..59491319,2	MCF-7	breast:
25	chr17:59489398..59491206-chr8:145752250..145753820,2	MCF-7	breast:
26	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
27	chr17:59489843..59492538-chr20:52557995..52559827,2	MCF-7	breast:
28	chr17:59490768..59492795-chr20:42086265..42087870,2	MCF-7	breast:
29	chr17:59489837..59492539-chr20:52768488..52770171,2	MCF-7	breast:
30	chr17:59489144..59491362-chr8:144700115..144701860,2	MCF-7	breast:
31	chr17:59490269..59492891-chr17:73768082..73769932,2	MCF-7	breast:
32	chr17:59489294..59491290-chr3:1177376..1179707,2	MCF-7	breast:
33	chr16:729895..731723-chr17:59489469..59491172,2	MCF-7	breast:
34	chr17:59489238..59492668-chr17:59650942..59653805,58	MCF-7	breast:
35	chr17:59489427..59492418-chr17:59944294..59946744,2	MCF-7	breast:
36	chr17:59490880..59491389-chr17:59540868..59541574,2	MCF-7	breast:
37	chr1:112527808..112533804-chr17:59487383..59491538,7	MCF-7	breast:
38	chr17:59488637..59491687-chr20:49346765..49351004,5	MCF-7	breast:
39	chr17:59490422..59491178-chr20:49410926..49411541,2	MCF-7	breast:
40	chr17:59085731..59087853-chr17:59489578..59492424,2	MCF-7	breast:
41	chr17:59489269..59491271-chr20:46301463..46303780,2	MCF-7	breast:
42	chr17:59484671..59491871-chr20:55837745..55844407,10	MCF-7	breast:
43	chr17:59490733..59491562-chr20:49411114..49411874,2	MCF-7	breast:
44	chr1:112529769..112535605-chr17:59484879..59491283,15	MCF-7	breast:
45	chr17:59490904..59493858-chr5:81572794..81575325,2	MCF-7	breast:
46	chr17:59076528..59085339-chr17:59484802..59491356,15	MCF-7	breast:
47	chr17:59486918..59494123-chr20:45984608..45990861,17	MCF-7	breast:
48	chr17:59490326..59492586-chr17:59938992..59941381,2	MCF-7	breast:
49	chr17:59489526..59491769-chr17:59745593..59747850,2	MCF-7	breast:
50	chr17:59486255..59492170-chr17:59932286..59941695,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267280	TF binding region
ENSG00000124151	Chromatin interaction
ENSG00000103266	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000181163	Chromatin interaction
ENSG00000124193	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000247828	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000254249	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000242622	Chromatin interaction
ENSG00000205464	Chromatin interaction
ENSG00000104522	Chromatin interaction
ENSG00000264853	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000103326	Chromatin interaction
ENSG00000164180	Chromatin interaction
ENSG00000082701	Chromatin interaction
ENSG00000181171	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000254402	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000186468	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000112624	Chromatin interaction
ENSG00000171385	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000231437	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1010270	1.00[JPT][hapmap]
rs10515196	1.00[JPT][hapmap]
rs16945174	1.00[JPT][hapmap]
rs16945232	1.00[JPT][hapmap]
rs16945233	1.00[JPT][hapmap]
rs2286528	0.85[ASW][hapmap];0.97[LWK][hapmap]
rs3785838	1.00[JPT][hapmap]
rs57045595	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58036240	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58832799	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59382073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59430864	1.00[ASN][1000 genomes]
rs60549606	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61068714	0.83[ASN][1000 genomes]
rs61764069	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7211156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs730562	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs734375	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73991913	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73991919	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs758600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv908664	chr17:59465697-59491030	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	261 gene(s)	inside rSNPs	diseases
8	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
9	nsv908667	chr17:59471151-59491030	Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	256 gene(s)	inside rSNPs	diseases
10	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
11	nsv908669	chr17:59471372-59491030	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59489600-59491200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr17:59490200-59491400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr17:59490200-59491600	Weak transcription	Hela-S3	cervix
4	chr17:59490200-59493800	Weak transcription	K562	blood
5	chr17:59490400-59493600	Weak transcription	HSMMtube	muscle
6	chr17:59490400-59493800	Weak transcription	Liver	Liver
7	chr17:59490600-59491200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:59490600-59491200	Flanking Active TSS	Osteobl	bone
9	chr17:59490600-59491800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:59490600-59493800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr17:59490600-59493800	Weak transcription	Brain Angular Gyrus	brain
12	chr17:59490600-59493800	Weak transcription	Gastric	stomach
13	chr17:59490600-59494000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr17:59490600-59494000	Weak transcription	Esophagus	oesophagus
15	chr17:59490600-59494000	Weak transcription	HMEC	breast
16	chr17:59490600-59494200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr17:59490600-59494200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:59490800-59491200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr17:59490800-59491200	Active TSS	NHLF	lung
20	chr17:59490800-59491400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:59490800-59491400	Flanking Active TSS	HepG2	liver
22	chr17:59490800-59491600	Weak transcription	Left Ventricle	heart
23	chr17:59490800-59491600	Weak transcription	Right Ventricle	heart
24	chr17:59490800-59492000	Enhancers	Ovary	ovary
25	chr17:59490800-59492600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr17:59490800-59493200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:59490800-59494000	Weak transcription	Brain Anterior Caudate	brain
28	chr17:59490800-59494000	Weak transcription	Brain Substantia Nigra	brain
29	chr17:59490800-59494000	Weak transcription	Pancreas	Pancrea
30	chr17:59491000-59491200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
31	chr17:59491000-59491200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr17:59491000-59491200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr17:59491000-59491200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr17:59491000-59491200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:59491000-59491200	Enhancers	Fetal Kidney	kidney
36	chr17:59491000-59491200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr17:59491000-59491400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:59491000-59491600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:59491000-59491600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr17:59491000-59491800	Bivalent Enhancer	Colonic Mucosa	Colon
41	chr17:59491000-59492000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:59491000-59492000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr17:59491000-59492000	Weak transcription	Aorta	Aorta
44	chr17:59491000-59492000	Active TSS	Fetal Lung	lung
45	chr17:59491000-59492200	Enhancers	Right Atrium	heart
46	chr17:59491000-59492400	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr17:59491000-59492400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr17:59491000-59493200	Weak transcription	NH-A	brain
49	chr17:59491000-59493600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:59491000-59493800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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