Variant report

Variant	rs17839547
Chromosome Location	chr16:30540035-30540036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30537047-30547480	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:30539890-30541214	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr16:30540013-30540977	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr16:30539800-30543244	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:30539957-30540833	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr16:30539908-30540880	GM12891	blood:	n/a	n/a
7	MTA3	chr16:30539832-30540890	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:30539882-30540851	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr16:30539965-30540925	GM12878	blood:	n/a	n/a
10	STAT5A	chr16:30539789-30540234	GM12878	blood:	n/a	n/a
11	POLR2A	chr16:30539861-30541105	PANC-1	pancreas:	n/a	n/a
12	HDAC2	chr16:30540011-30540288	K562	blood:	n/a	n/a
13	POLR2A	chr16:30540008-30540964	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:30540009-30540778	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr16:30540007-30541039	Raji	blood:	n/a	n/a
16	POLR2A	chr16:30539973-30540566	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr16:30539914-30541097	HepG2	liver:	n/a	n/a
18	POLR2A	chr16:30539965-30540948	GM12892	blood:	n/a	n/a
19	POLR2A	chr16:30539843-30541157	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr16:30539937-30541039	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr16:30539876-30540951	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr16:30539961-30540873	GM12878	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30453602..30463168-chr16:30533711..30543502,36	MCF-7	breast:
2	chr16:30535183..30540797-chr16:30579748..30584975,15	MCF-7	breast:
3	chr16:30534593..30542459-chr16:30576363..30586049,22	MCF-7	breast:
4	chr16:30537092..30540125-chr16:30618129..30621558,4	K562	blood:
5	chr16:30534557..30548684-chr16:30561877..30572653,49	MCF-7	breast:
6	chr16:30538377..30542208-chr16:30619614..30623452,7	MCF-7	breast:
7	chr16:30538416..30540910-chr16:30673584..30675872,2	MCF-7	breast:
8	chr16:30427799..30431834-chr16:30534294..30540593,7	MCF-7	breast:
9	chr1:149222310..149225092-chr16:30538220..30540895,2	MCF-7	breast:
10	chr16:30455473..30459331-chr16:30536494..30540885,5	K562	blood:
11	chr16:30537304..30542390-chr16:30581808..30586488,7	K562	blood:
12	chr16:30536695..30540828-chr16:30620519..30623235,5	MCF-7	breast:
13	chr16:30537916..30540494-chr16:30660265..30663617,4	K562	blood:
14	chr16:30520573..30524567-chr16:30535660..30540448,6	MCF-7	breast:
15	chr16:30462000..30465097-chr16:30539143..30541421,3	MCF-7	breast:
16	chr16:30537208..30540827-chr16:30710007..30712078,3	MCF-7	breast:
17	chr16:30537270..30540938-chr16:30667776..30670897,3	K562	blood:
18	chr16:30439037..30443694-chr16:30535718..30544524,17	MCF-7	breast:
19	chr16:30418091..30420983-chr16:30538453..30540538,2	MCF-7	breast:
20	chr16:30453263..30460635-chr16:30534974..30549190,40	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF768	TF binding region
ENSG00000260869	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000229809	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000156853	Chromatin interaction
ENSG00000005844	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000169951	Chromatin interaction
ENSG00000239791	Chromatin interaction
ENSG00000199787	Chromatin interaction
ENSG00000179965	Chromatin interaction
ENSG00000156858	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11574943	1.00[MEX][hapmap]
rs11860431	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11865041	1.00[AMR][1000 genomes]
rs11866017	1.00[AMR][1000 genomes]
rs11867032	0.83[AMR][1000 genomes]
rs17839542	1.00[MEX][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	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
4	nsv905726	chr16:30528272-30546488	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30538800-30540200	Weak transcription	Gastric	stomach
2	chr16:30538800-30540600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr16:30539200-30540600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr16:30539200-30540600	Enhancers	Right Atrium	heart
5	chr16:30539200-30540600	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr16:30539200-30540800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr16:30539200-30540800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:30539200-30540800	Enhancers	Esophagus	oesophagus
9	chr16:30539200-30540800	Enhancers	Fetal Muscle Trunk	muscle
10	chr16:30539200-30540800	Enhancers	Pancreas	Pancrea
11	chr16:30539200-30540800	Enhancers	Right Ventricle	heart
12	chr16:30539200-30541000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr16:30539200-30541000	Enhancers	Stomach Mucosa	stomach
14	chr16:30539200-30541600	Enhancers	Fetal Intestine Small	intestine
15	chr16:30539200-30542000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr16:30539200-30542000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr16:30539200-30542200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr16:30539200-30542200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr16:30539200-30542400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr16:30539200-30543600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:30539200-30543600	Weak transcription	Aorta	Aorta
22	chr16:30539200-30545200	Weak transcription	HSMM	muscle
23	chr16:30539400-30540200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr16:30539400-30540200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:30539400-30540200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr16:30539400-30540200	Enhancers	Colon Smooth Muscle	Colon
27	chr16:30539400-30540400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:30539400-30540400	Weak transcription	Left Ventricle	heart
29	chr16:30539400-30540600	Weak transcription	Fetal Brain Female	brain
30	chr16:30539400-30540600	Enhancers	Fetal Intestine Large	intestine
31	chr16:30539400-30540800	Enhancers	Primary B cells from peripheral blood	blood
32	chr16:30539400-30540800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr16:30539400-30540800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr16:30539400-30540800	Enhancers	Fetal Muscle Leg	muscle
35	chr16:30539400-30540800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr16:30539400-30540800	Enhancers	Dnd41	blood
37	chr16:30539400-30540800	Enhancers	HMEC	breast
38	chr16:30539400-30541000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr16:30539400-30541000	Enhancers	Fetal Thymus	thymus
40	chr16:30539400-30541000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr16:30539400-30541000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr16:30539400-30541600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr16:30539400-30541800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr16:30539400-30541800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr16:30539400-30541800	Weak transcription	Brain Germinal Matrix	brain
46	chr16:30539400-30541800	Weak transcription	Brain Hippocampus Middle	brain
47	chr16:30539400-30542000	Enhancers	Placenta	Placenta
48	chr16:30539400-30542200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr16:30539400-30542200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr16:30539400-30542400	Enhancers	Liver	Liver

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