Variant report

Variant	rs17790906
Chromosome Location	chr16:30569659-30569660
allele	G/T
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	YY1	chr16:30569307-30570018	GM12892	blood:	n/a	chr16:30569713-30569723 chr16:30569803-30569825 chr16:30569701-30569723 chr16:30569706-30569725 chr16:30569718-30569727 chr16:30569814-30569822 chr16:30569815-30569825 chr16:30569713-30569723 chr16:30569808-30569827 chr16:30569711-30569723 chr16:30569721-30569730
2	CCNT2	chr16:30569205-30570100	K562	blood:	n/a	n/a
3	CTCF	chr16:30569597-30570039	K562	blood:	n/a	chr16:30569641-30569649
4	POLR2A	chr16:30569519-30570197	HCT-116	colon:	n/a	n/a
5	POLR2A	chr16:30569347-30570202	MCF10A-Er-Src	breast:	n/a	n/a
6	TAF1	chr16:30569554-30569919	GM12891	blood:	n/a	n/a
7	TAF1	chr16:30569307-30570162	A549	lung:	n/a	n/a
8	JUND	chr16:30569613-30570211	A549	lung:	n/a	chr16:30569825-30569836 chr16:30569826-30569836
9	SIN3AK20	chr16:30569283-30570237	MCF-7	breast:	n/a	n/a
10	SMC3	chr16:30569620-30569758	K562	blood:	n/a	n/a
11	POLR2A	chr16:30569493-30570214	K562	blood:	n/a	n/a
12	REST	chr16:30568725-30570431	H1-neurons	neurons:	n/a	chr16:30568881-30568889
13	POLR2A	chr16:30568681-30570222	Raji	blood:	n/a	n/a
14	SIN3AK20	chr16:30569386-30570169	K562	blood:	n/a	n/a
15	YY1	chr16:30569020-30570097	GM12892	blood:	n/a	chr16:30569713-30569723 chr16:30569803-30569825 chr16:30569701-30569723 chr16:30569706-30569725 chr16:30569718-30569727 chr16:30569814-30569822 chr16:30569815-30569825 chr16:30569713-30569723 chr16:30569808-30569827 chr16:30569711-30569723 chr16:30569210-30569221 chr16:30569721-30569730
16	NFIC	chr16:30569369-30570246	HepG2	liver:	n/a	n/a
17	MAX	chr16:30568968-30570433	HCT-116	colon:	n/a	n/a
18	YY1	chr16:30569358-30570273	ECC-1	luminal epithelium:	n/a	chr16:30569713-30569723 chr16:30569803-30569825 chr16:30569701-30569723 chr16:30569706-30569725 chr16:30569718-30569727 chr16:30569814-30569822 chr16:30569815-30569825 chr16:30569713-30569723 chr16:30569808-30569827 chr16:30569711-30569723 chr16:30569721-30569730
19	EGR1	chr16:30569290-30570392	HCT-116	colon:	n/a	chr16:30570142-30570153
20	EBF1	chr16:30569577-30569900	GM12878	blood:	n/a	n/a
21	EP300	chr16:30569612-30570250	K562	blood:	n/a	n/a
22	ELF1	chr16:30569361-30570244	MCF-7	breast:	n/a	chr16:30569718-30569727
23	MAX	chr16:30569538-30570054	A549	lung:	n/a	n/a
24	SP1	chr16:30569473-30570129	GM12878	blood:	n/a	n/a
25	ARID3A	chr16:30569585-30570169	K562	blood:	n/a	n/a
26	NR2C2	chr16:30569510-30569962	Hela-S3	cervix:	n/a	chr16:30569735-30569750 chr16:30569738-30569747 chr16:30569736-30569749
27	RCOR1	chr16:30569331-30570183	HepG2	liver:	n/a	n/a
28	POLR2A	chr16:30569395-30570205	K562	blood:	n/a	n/a
29	CTCF	chr16:30569560-30569710	HUVEC	blood vessel:	n/a	chr16:30569641-30569649
30	ATF1	chr16:30569613-30570230	K562	blood:	n/a	n/a
31	ZBTB33	chr16:30569548-30570196	HCT-116	colon:	n/a	n/a
32	MYC	chr16:30569580-30570045	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr16:30569525-30570160	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr16:30569172-30570310	U87	brain:	n/a	n/a
35	USF1	chr16:30569541-30569896	A549	lung:	n/a	n/a
36	ETS1	chr16:30569423-30570026	K562	blood:	n/a	n/a
37	FOXA2	chr16:30569622-30570115	HepG2	liver:	n/a	n/a
38	GABPA	chr16:30569587-30569940	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr16:30569520-30569670	GM06990	blood:	n/a	chr16:30569641-30569649
40	FOS	chr16:30569608-30570018	MCF10A-Er-Src	breast:	n/a	chr16:30569826-30569836
41	POLR2A	chr16:30569276-30570350	H1-hESC	embryonic stem cell:	n/a	n/a
42	TEAD4	chr16:30569493-30570419	K562	blood:	n/a	n/a
43	POLR2A	chr16:30569322-30570320	HUVEC	blood vessel:	n/a	n/a
44	ZBTB7A	chr16:30569219-30569967	ECC-1	luminal epithelium:	n/a	chr16:30569222-30569230 chr16:30569624-30569632
45	BHLHE40	chr16:30569517-30570029	GM12878	blood:	n/a	n/a
46	ELF1	chr16:30569435-30570089	MCF-7	breast:	n/a	chr16:30569718-30569727
47	POLR2A	chr16:30569139-30570161	GM18526	blood:	n/a	n/a
48	POLR2A	chr16:30568718-30570160	GM12891	blood:	n/a	n/a
49	E2F4	chr16:30569429-30570035	K562	blood:	n/a	chr16:30569721-30569730
50	POLR2A	chr16:30569201-30569776	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30455450..30458862-chr16:30569304..30572069,4	K562	blood:
2	chr16:30567563..30571772-chr16:30581766..30584287,7	MCF-7	breast:
3	chr16:30545977..30548808-chr16:30568240..30572636,5	K562	blood:
4	chr16:30514339..30516665-chr16:30568095..30569854,2	K562	blood:
5	chr16:30545877..30546777-chr16:30569372..30569939,2	MCF-7	breast:
6	chr16:30534557..30548684-chr16:30561877..30572653,49	MCF-7	breast:
7	chr16:30545944..30548930-chr16:30568116..30571083,5	K562	blood:
8	chr16:30569565..30570310-chr17:41115952..41116748,2	Hela-S3	cervix:
9	chr16:30566138..30571776-chr16:30580042..30586389,14	K562	blood:
10	chr16:30567962..30575227-chr16:30576961..30586002,21	MCF-7	breast:
11	chr16:30440234..30443993-chr16:30568188..30571380,4	MCF-7	breast:
12	chr16:30456820..30459017-chr16:30567139..30569757,2	MCF-7	breast:
13	chr16:30568302..30571284-chr16:30621692..30624575,2	MCF-7	breast:
14	chr16:30569322..30571012-chr16:30595108..30597618,2	K562	blood:
15	chr16:30405223..30408007-chr16:30567849..30569998,3	MCF-7	breast:
16	chr16:30569328..30570273-chr16:30583071..30583783,3	MCF-7	breast:
17	chr16:30536717..30540030-chr16:30566020..30569997,3	K562	blood:
18	chr16:30568530..30574160-chr16:30594464..30599047,9	MCF-7	breast:
19	chr16:30568254..30570090-chr16:30667629..30670948,3	K562	blood:
20	chr16:30440010..30443715-chr16:30568872..30571255,4	MCF-7	breast:
21	chr16:30568317..30569901-chr16:30597134..30598772,2	MCF-7	breast:
22	chr16:30455870..30458862-chr16:30569304..30571226,2	K562	blood:
23	chr16:30568081..30571222-chr16:30660229..30663794,5	K562	blood:
24	chr16:30546047..30547051-chr16:30568755..30570523,5	MCF-7	breast:
25	chr16:30567520..30571513-chr16:30580042..30586732,13	K562	blood:

Variant related genes	Relation type
ZNF764	TF binding region
ENSG00000260869	TF binding region
ENSG00000179918	Chromatin interaction
ENSG00000156853	Chromatin interaction
ENSG00000260167	Chromatin interaction
ENSG00000005844	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000266967	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000156858	Chromatin interaction
ENSG00000239791	Chromatin interaction
ENSG00000229809	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000266305	Chromatin interaction
ENSG00000261459	Chromatin interaction
ENSG00000235560	Chromatin interaction
ENSG00000197162	Chromatin interaction
ENSG00000169955	Chromatin interaction
ENSG00000180035	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11862597	1.00[GIH][hapmap]
rs17839544	1.00[GIH][hapmap]
rs2230434	1.00[GIH][hapmap];0.92[TSI][hapmap]
rs56311083	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72793343	0.82[EUR][1000 genomes]
rs8056929	0.82[MEX][hapmap]
rs8063005	0.85[CEU][hapmap]
rs9934579	1.00[GIH][hapmap]
rs9934806	0.85[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	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	nsv905727	chr16:30564526-30689696	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17790906	SPN	cis	parietal	SCAN
rs17790906	ZNF764	cis	Skin Sun Exposed Lower leg	GTEx
rs17790906	ZNF843	cis	cerebellum	SCAN
rs17790906	DCTPP1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30568400-30570000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:30568400-30570000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr16:30568400-30570000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr16:30568400-30570200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr16:30568400-30570400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:30568400-30570400	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr16:30568400-30570400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr16:30568400-30570400	Active TSS	Fetal Brain Female	brain
9	chr16:30568600-30569800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:30568600-30569800	Active TSS	Lung	lung
11	chr16:30568600-30570000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr16:30568600-30570000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:30568600-30570000	Active TSS	Fetal Intestine Large	intestine
14	chr16:30568600-30570000	Active TSS	GM12878-XiMat	blood
15	chr16:30568600-30570000	Active TSS	NHLF	lung
16	chr16:30568600-30570200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr16:30568600-30570200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:30568600-30570200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr16:30568600-30570200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr16:30568600-30570200	Active TSS	Pancreas	Pancrea
21	chr16:30568600-30570200	Active TSS	HSMM	muscle
22	chr16:30568600-30570200	Active TSS	HSMMtube	muscle
23	chr16:30568600-30570200	Active TSS	NHDF-Ad	bronchial
24	chr16:30568600-30570400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr16:30568600-30570400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr16:30568600-30570400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:30568600-30570400	Active TSS	Osteobl	bone
28	chr16:30568800-30569800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr16:30568800-30569800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:30568800-30569800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
31	chr16:30568800-30569800	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr16:30568800-30569800	Active TSS	Small Intestine	intestine
33	chr16:30568800-30570000	Active TSS	Primary T cells from cord blood	blood
34	chr16:30568800-30570000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr16:30568800-30570000	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr16:30568800-30570000	Active TSS	Fetal Heart	heart
37	chr16:30568800-30570000	Active TSS	Fetal Intestine Small	intestine
38	chr16:30568800-30570000	Active TSS	Stomach Mucosa	stomach
39	chr16:30568800-30570200	Active TSS	H9 Cell Line	embryonic stem cell
40	chr16:30568800-30570200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr16:30568800-30570200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr16:30568800-30570200	Active TSS	Esophagus	oesophagus
43	chr16:30568800-30570200	Active TSS	Fetal Kidney	kidney
44	chr16:30568800-30570200	Active TSS	Gastric	stomach
45	chr16:30568800-30570200	Active TSS	Left Ventricle	heart
46	chr16:30568800-30570200	Active TSS	Ovary	ovary
47	chr16:30568800-30570200	Active TSS	Right Ventricle	heart
48	chr16:30568800-30570400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr16:30568800-30570400	Active TSS	Brain Substantia Nigra	brain
50	chr16:30568800-30570400	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links