Variant report

Variant	rs4985816
Chromosome Location	chr17:20901713-20901714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:90)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:90 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr17:20899864-20904071	HepG2	liver:	n/a	chr17:20902795-20902805 chr17:20902795-20902805 chr17:20902795-20902805 chr17:20902204-20902216
2	KAP1	chr17:20901283-20901791	HEK293	kidney:	n/a	n/a
3	POLR2A	chr17:20901604-20901912	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:20899351-20909849	K562	blood:	n/a	n/a
5	POLR2A	chr17:20900490-20903179	K562	blood:	n/a	n/a
6	POLR2A	chr17:20901407-20902768	HL-60	blood:	n/a	n/a
7	POLR2A	chr17:20901052-20902950	GM12891	blood:	n/a	n/a
8	POLR2A	chr17:20899206-20903031	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr17:20900967-20901889	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr17:20900814-20902988	GM12878	blood:	n/a	n/a
11	NFATC1	chr17:20900906-20902881	GM12878	blood:	n/a	chr17:20902246-20902259
12	POLR2A	chr17:20900994-20903050	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:20901226-20902882	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr17:20901121-20902989	HCT-116	colon:	n/a	n/a
15	RCOR1	chr17:20901650-20901755	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr17:20899538-20902748	U87	brain:	n/a	n/a
17	JUND	chr17:20900984-20902063	A549	lung:	n/a	n/a
18	POLR2A	chr17:20900597-20902264	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr17:20900827-20901962	A549	lung:	n/a	n/a
20	POLR2A	chr17:20900462-20902080	HepG2	liver:	n/a	n/a
21	SIN3AK20	chr17:20900728-20902534	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr17:20900886-20902025	GM19193	blood:	n/a	n/a
23	SIN3AK20	chr17:20901401-20902157	A549	lung:	n/a	n/a
24	POLR2A	chr17:20900826-20901956	A549	lung:	n/a	n/a
25	TCF12	chr17:20901171-20902143	A549	lung:	n/a	n/a
26	POLR2A	chr17:20900273-20901981	U87	brain:	n/a	n/a
27	POLR2A	chr17:20900718-20903554	H1-hESC	embryonic stem cell:	n/a	n/a
28	BCL3	chr17:20900503-20902569	A549	lung:	n/a	n/a
29	POLR2A	chr17:20900974-20902342	HUVEC	blood vessel:	n/a	n/a
30	MTA3	chr17:20900675-20902913	GM12878	blood:	n/a	n/a
31	POLR2A	chr17:20899537-20902909	ECC-1	luminal epithelium:	n/a	n/a
32	HMGN3	chr17:20901249-20901822	K562	blood:	n/a	n/a
33	POLR2A	chr17:20901616-20902177	GM12878	blood:	n/a	n/a
34	BCL3	chr17:20901646-20902196	GM12878	blood:	n/a	n/a
35	POLR2A	chr17:20900921-20902164	GM12878	blood:	n/a	n/a
36	POLR2A	chr17:20901100-20902969	HL-60	blood:	n/a	n/a
37	POLR2A	chr17:20900596-20902478	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr17:20900755-20901893	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr17:20899493-20903025	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr17:20900348-20902998	K562	blood:	n/a	n/a
41	POLR2A	chr17:20901019-20902125	H1-hESC	embryonic stem cell:	n/a	n/a
42	STAT5A	chr17:20901037-20901854	GM12878	blood:	n/a	n/a
43	POLR2A	chr17:20900309-20902722	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr17:20901174-20902992	K562	blood:	n/a	n/a
45	POLR2A	chr17:20901096-20902968	H1-neurons	neurons:	n/a	n/a
46	POLR2A	chr17:20901272-20902752	HCT-116	colon:	n/a	n/a
47	POLR2A	chr17:20901146-20903014	GM12892	blood:	n/a	n/a
48	POLR2A	chr17:20901200-20903533	GM12891	blood:	n/a	n/a
49	POLR2A	chr17:20901321-20906277	GM12892	blood:	n/a	n/a
50	POLR2A	chr17:20901480-20902748	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:20901201..20904612-chr17:20905901..20908917,4	MCF-7	breast:
2	chr17:20900050..20901935-chr17:20907536..20910241,2	MCF-7	breast:
3	chr17:20899990..20902443-chr17:20946128..20948088,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263986	TF binding region
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1045162	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1127814	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12051606	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12600703	0.91[AMR][1000 genomes]
rs12601292	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12602058	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12943067	0.80[ASN][1000 genomes]
rs12946114	0.84[ASN][1000 genomes]
rs1542552	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17770614	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054464	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2127095	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291034	0.97[ASN][1000 genomes]
rs2364326	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886105	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4445951	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985811	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985814	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985815	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985959	0.90[ASN][1000 genomes]
rs4985963	0.85[ASN][1000 genomes]
rs4985966	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985967	0.80[ASN][1000 genomes]
rs4985968	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985969	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985970	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985971	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4985975	0.91[AMR][1000 genomes]
rs56323013	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58235085	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59543297	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59713572	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587111	0.82[ASN][1000 genomes]
rs6618	0.90[ASN][1000 genomes]
rs719093	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7209129	0.87[ASN][1000 genomes]
rs7216921	0.89[ASN][1000 genomes]
rs880653	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899337	0.90[AMR][1000 genomes]
rs899340	0.89[ASN][1000 genomes]
rs9911289	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv960442	chr17:20901168-20903702	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4985816	RP11-344E13.3	cis	lung	GTEx
rs4985816	RP11-344E13.3	cis	Whole Blood	GTEx
rs4985816	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs4985816	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4985816	RP11-344E13.3	cis	Artery Tibial	GTEx
rs4985816	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs4985816	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs4985816	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs4985816	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs4985816	RP11-344E13.3	cis	Stomach	GTEx
rs4985816	RP11-344E13.3	cis	Thyroid	GTEx
rs4985816	RP11-344E13.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20896400-20902800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:20896600-20901800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:20896600-20901800	Weak transcription	HUVEC	blood vessel
4	chr17:20896600-20902000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr17:20896600-20906800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:20896800-20901800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:20896800-20901800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:20896800-20901800	Weak transcription	NHDF-Ad	bronchial
9	chr17:20896800-20902200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr17:20896800-20902200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:20896800-20902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr17:20896800-20902200	Weak transcription	Fetal Thymus	thymus
13	chr17:20896800-20902400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr17:20896800-20902600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:20896800-20902600	Weak transcription	Colonic Mucosa	Colon
16	chr17:20896800-20902600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr17:20896800-20902600	Weak transcription	NHEK	skin
18	chr17:20896800-20904200	Weak transcription	Primary T cells from cord blood	blood
19	chr17:20896800-20904800	Weak transcription	Fetal Kidney	kidney
20	chr17:20896800-20905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:20897000-20901800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:20897000-20901800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr17:20897000-20901800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr17:20897000-20901800	Weak transcription	Fetal Heart	heart
25	chr17:20897000-20901800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:20897000-20902000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:20897000-20902000	Weak transcription	Osteobl	bone
28	chr17:20897000-20902400	Weak transcription	HMEC	breast
29	chr17:20897000-20902600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr17:20897000-20902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:20897000-20902600	Weak transcription	Pancreas	Pancrea
32	chr17:20897000-20902800	Weak transcription	HepG2	liver
33	chr17:20897000-20903400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr17:20897000-20905200	Weak transcription	Fetal Brain Male	brain
35	chr17:20897200-20901800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr17:20897200-20902000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:20897200-20904600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:20897600-20902400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr17:20897600-20902400	Weak transcription	NH-A	brain
40	chr17:20897800-20902000	Weak transcription	Fetal Intestine Large	intestine
41	chr17:20897800-20902200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:20897800-20902400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr17:20898000-20901800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr17:20898000-20902600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:20898000-20905000	Weak transcription	Hela-S3	cervix
46	chr17:20898200-20902200	Weak transcription	Placenta	Placenta
47	chr17:20898400-20902800	Weak transcription	Stomach Mucosa	stomach
48	chr17:20899200-20908600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr17:20899400-20902000	Enhancers	Spleen	Spleen
50	chr17:20899600-20902600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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