Variant report

Variant	rs3797339
Chromosome Location	chr5:118691693-118691694
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	POLR2A	chr5:118688526-118696061	GM12878	blood:	n/a	n/a
2	SIN3A	chr5:118691303-118692554	GM12878	blood:	n/a	chr5:118691638-118691649
3	MAX	chr5:118691230-118692029	ECC-1	luminal epithelium:	n/a	n/a
4	HA-E2F1	chr5:118690803-118691952	MCF-7	breast:	n/a	chr5:118691641-118691653 chr5:118690878-118690887
5	MXI1	chr5:118691182-118692384	IMR90	lung:	n/a	n/a
6	POLR2A	chr5:118690622-118693443	GM19193	blood:	n/a	n/a
7	MAX	chr5:118691353-118691936	MCF-7	breast:	n/a	n/a
8	ELF1	chr5:118691233-118691939	GM12878	blood:	n/a	chr5:118691519-118691528
9	TCF12	chr5:118691346-118691916	ECC-1	luminal epithelium:	n/a	n/a
10	MTA3	chr5:118691072-118692474	GM12878	blood:	n/a	n/a
11	TAF1	chr5:118691513-118691842	GM12891	blood:	n/a	n/a
12	PAX5	chr5:118691220-118691896	GM12878	blood:	n/a	n/a
13	RELA	chr5:118690557-118694108	GM12891	blood:	n/a	n/a
14	TBP	chr5:118689422-118692594	GM12878	blood:	n/a	n/a
15	POU2F2	chr5:118691186-118691958	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:118691664-118691954	H1-neurons	neurons:	n/a	n/a
17	EP300	chr5:118691333-118691838	GM12878	blood:	n/a	chr5:118691519-118691535 chr5:118691535-118691551 chr5:118691522-118691538 chr5:118691374-118691388
18	TBL1XR1	chr5:118691149-118692499	GM12878	blood:	n/a	n/a
19	TAF1	chr5:118691281-118691889	GM12892	blood:	n/a	n/a
20	MAZ	chr5:118690555-118692953	IMR90	lung:	n/a	chr5:118692461-118692472
21	CUX1	chr5:118691203-118691794	GM12878	blood:	n/a	n/a
22	E2F6	chr5:118691375-118691956	H1-hESC	embryonic stem cell:	n/a	chr5:118691641-118691653
23	PML	chr5:118690397-118693186	GM12878	blood:	n/a	chr5:118692075-118692083
24	YY1	chr5:118691668-118691959	H1-hESC	embryonic stem cell:	n/a	n/a
25	POU2F2	chr5:118691367-118692059	GM12891	blood:	n/a	chr5:118691998-118692010
26	POLR2A	chr5:118691512-118692024	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr5:118690288-118692832	GM12892	blood:	n/a	n/a
28	YY1	chr5:118691330-118692157	GM12878	blood:	n/a	chr5:118691519-118691528
29	MEF2A	chr5:118691239-118691846	GM12878	blood:	n/a	chr5:118691333-118691347
30	RELA	chr5:118691166-118692619	GM19099	blood:	n/a	n/a
31	NFATC1	chr5:118690799-118691972	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:118690266-118692633	GM12892	blood:	n/a	n/a
33	SIN3AK20	chr5:118691641-118691921	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:118690639-118692349	GM12878	blood:	n/a	n/a
35	USF2	chr5:118691439-118691854	GM12878	blood:	n/a	chr5:118691457-118691473 chr5:118691449-118691465
36	EP300	chr5:118691420-118691794	GM12878	blood:	n/a	chr5:118691519-118691535 chr5:118691535-118691551 chr5:118691522-118691538
37	POLR2A	chr5:118690511-118692628	GM12892	blood:	n/a	n/a
38	MAX	chr5:118691298-118692080	GM12878	blood:	n/a	n/a
39	RELA	chr5:118691236-118692556	GM12878	blood:	n/a	n/a
40	TCF12	chr5:118691327-118691807	GM12878	blood:	n/a	n/a
41	EGR1	chr5:118691412-118691734	ECC-1	luminal epithelium:	n/a	chr5:118691552-118691566
42	NFIC	chr5:118691314-118692629	GM12878	blood:	n/a	n/a
43	RELA	chr5:118690644-118693165	GM10847	blood:	n/a	n/a
44	MYC	chr5:118691376-118691955	H1-hESC	embryonic stem cell:	n/a	n/a
45	RELA	chr5:118691140-118692574	GM15510	blood:	n/a	n/a
46	POLR2A	chr5:118691561-118691897	H1-neurons	neurons:	n/a	n/a
47	TAF1	chr5:118691284-118691987	GM12878	blood:	n/a	n/a
48	CHD1	chr5:118688941-118694425	GM12878	blood:	n/a	n/a
49	JUND	chr5:118690972-118691901	H1-hESC	embryonic stem cell:	n/a	n/a
50	BCL3	chr5:118691275-118691906	GM12878	blood:	n/a	chr5:118691526-118691539 chr5:118691546-118691559 chr5:118691527-118691540

Variant related genes	Relation type
TNFAIP8	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10477585	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1112247	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13155880	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1396609	0.82[AFR][1000 genomes]
rs17145265	0.85[AFR][1000 genomes]
rs250298	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs250299	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs250308	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32653	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32655	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32657	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32658	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3797341	0.88[AFR][1000 genomes]
rs3797343	0.88[AFR][1000 genomes]
rs3813308	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3920174	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs408095	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67328001	0.83[AFR][1000 genomes]
rs6863311	0.86[AFR][1000 genomes]
rs6869512	0.86[AFR][1000 genomes]
rs6870253	0.80[AFR][1000 genomes]
rs6876224	0.85[AFR][1000 genomes]
rs6877025	0.86[AFR][1000 genomes]
rs6882237	0.86[AFR][1000 genomes]
rs6891084	0.84[AFR][1000 genomes]
rs6896277	0.85[AFR][1000 genomes]
rs6896553	0.85[AFR][1000 genomes]
rs6896559	0.85[AFR][1000 genomes]
rs6897359	0.80[AFR][1000 genomes]
rs7707470	0.85[AFR][1000 genomes]
rs996934	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118671200-118695400	Weak transcription	A549	lung
2	chr5:118682600-118693600	Weak transcription	Dnd41	blood
3	chr5:118684000-118692800	Weak transcription	K562	blood
4	chr5:118689600-118692000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr5:118690400-118692600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr5:118690600-118691800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:118690600-118691800	Active TSS	HepG2	liver
8	chr5:118690600-118692000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:118690600-118692400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:118690600-118693200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr5:118690600-118693400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr5:118690600-118700400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:118690800-118692200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:118690800-118692200	Flanking Active TSS	Thymus	Thymus
15	chr5:118690800-118692400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:118690800-118692400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr5:118690800-118692400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:118690800-118693800	Active TSS	Rectal Smooth Muscle	rectum
19	chr5:118691000-118691800	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr5:118691000-118692000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr5:118691000-118692000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr5:118691000-118692200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:118691000-118692200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr5:118691000-118692200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:118691000-118692400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr5:118691000-118692400	Active TSS	Esophagus	oesophagus
27	chr5:118691000-118692600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr5:118691000-118692600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr5:118691000-118692600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:118691000-118692600	Flanking Active TSS	HUVEC	blood vessel
31	chr5:118691000-118692600	Active TSS	Osteobl	bone
32	chr5:118691000-118693000	Bivalent/Poised TSS	Psoas Muscle	Psoas
33	chr5:118691000-118693000	Active TSS	Right Ventricle	heart
34	chr5:118691000-118693400	Active TSS	HSMMtube	muscle
35	chr5:118691200-118691800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr5:118691200-118691800	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr5:118691200-118691800	Active TSS	Placenta	Placenta
38	chr5:118691200-118692000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:118691200-118692000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:118691200-118692000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:118691200-118692000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr5:118691200-118692000	Active TSS	Hela-S3	cervix
43	chr5:118691200-118692200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr5:118691200-118692200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr5:118691200-118692200	Active TSS	Small Intestine	intestine
46	chr5:118691200-118692400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:118691200-118692400	Active TSS	Brain Anterior Caudate	brain
48	chr5:118691200-118692400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:118691200-118692400	Active TSS	Fetal Stomach	stomach
50	chr5:118691200-118692600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links