Variant report

Variant	rs28362660
Chromosome Location	chr1:78470246-78470247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:326)
CpG islands
(count:0)
Chromatin interactive
region (count:46)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:326 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr1:78468615-78470834	K562	blood:	n/a	chr1:78469262-78469276
2	TEAD4	chr1:78469982-78470267	HepG2	liver:	n/a	n/a
3	TCF7L2	chr1:78469981-78470686	HEK293	kidney:	n/a	chr1:78470252-78470268
4	POLR2A	chr1:78469623-78470998	Hela-S3	cervix:	n/a	n/a
5	BCLAF1	chr1:78469639-78470760	GM12878	blood:	n/a	n/a
6	ELK1	chr1:78469105-78470507	K562	blood:	n/a	n/a
7	PBX3	chr1:78469753-78470296	A549	lung:	n/a	n/a
8	POLR2A	chr1:78469699-78470355	SK-N-SH	brain:	n/a	n/a
9	CREB1	chr1:78469885-78470814	HepG2	liver:	n/a	n/a
10	CUX1	chr1:78469667-78470884	GM12878	blood:	n/a	n/a
11	CUX1	chr1:78469723-78471430	K562	blood:	n/a	n/a
12	ATF2	chr1:78469908-78470689	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr1:78469704-78470713	HepG2	liver:	n/a	n/a
14	IRF4	chr1:78470228-78470700	GM12878	blood:	n/a	n/a
15	TEAD4	chr1:78469579-78471022	K562	blood:	n/a	n/a
16	ATF2	chr1:78469560-78471024	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:78469594-78470926	GM18951	blood:	n/a	n/a
18	SRF	chr1:78469691-78470967	HCT-116	colon:	n/a	n/a
19	CBX3	chr1:78469700-78470848	HCT-116	colon:	n/a	n/a
20	ZMIZ1	chr1:78469600-78470842	K562	blood:	n/a	n/a
21	HEY1	chr1:78469606-78470943	K562	blood:	n/a	n/a
22	FOXM1	chr1:78469555-78470731	GM12878	blood:	n/a	n/a
23	CEBPZ	chr1:78469837-78470303	HepG2	liver:	n/a	n/a
24	SP1	chr1:78469662-78470423	K562	blood:	n/a	n/a
25	MAX	chr1:78469553-78470923	HCT-116	colon:	n/a	n/a
26	POLR2A	chr1:78469609-78470900	HCT-116	colon:	n/a	n/a
27	MAFK	chr1:78468708-78470928	K562	blood:	n/a	chr1:78469158-78469172 chr1:78469157-78469173 chr1:78469162-78469171 chr1:78469155-78469175 chr1:78469154-78469169 chr1:78469159-78469168 chr1:78469155-78469166
28	POLR2A	chr1:78469580-78470939	GM12891	blood:	n/a	n/a
29	MEF2A	chr1:78469621-78470367	K562	blood:	n/a	chr1:78469831-78469852 chr1:78469831-78469852 chr1:78469838-78469847
30	TAF1	chr1:78469742-78470760	K562	blood:	n/a	n/a
31	POU2F2	chr1:78469612-78470836	GM12878	blood:	n/a	chr1:78469866-78469878
32	BCL3	chr1:78469490-78470767	K562	blood:	n/a	n/a
33	JUND	chr1:78469623-78470892	HCT-116	colon:	n/a	n/a
34	POLR2A	chr1:78469196-78471142	K562	blood:	n/a	n/a
35	GTF2F1	chr1:78469956-78470529	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:78469633-78470832	GM12878	blood:	n/a	n/a
37	CTCF	chr1:78469782-78470694	K562	blood:	n/a	n/a
38	POLR2A	chr1:78469927-78470872	H1-neurons	neurons:	n/a	n/a
39	BRCA1	chr1:78469666-78470786	Hela-S3	cervix:	n/a	n/a
40	USF1	chr1:78469964-78470295	A549	lung:	n/a	n/a
41	MBD4	chr1:78469888-78470557	HepG2	liver:	n/a	n/a
42	SP4	chr1:78469939-78470419	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZBTB33	chr1:78469842-78470347	HCT-116	colon:	n/a	n/a
44	MAZ	chr1:78469682-78470895	K562	blood:	n/a	n/a
45	POLR2A	chr1:78469814-78470372	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:78469572-78470923	SK-N-MC	brain:	n/a	n/a
47	STAT3	chr1:78469995-78471019	MCF10A-Er-Src	breast:	n/a	chr1:78470132-78470140
48	MEF2C	chr1:78469558-78470566	GM12878	blood:	n/a	chr1:78469831-78469852 chr1:78469831-78469852 chr1:78470405-78470413 chr1:78469838-78469847
49	ZNF143	chr1:78469193-78470824	K562	blood:	n/a	chr1:78469862-78469880
50	STAT3	chr1:78469555-78471035	Hela-S3	cervix:	n/a	chr1:78470132-78470140

No data

(count:46 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78222274..78226935-chr1:78467368..78471641,7	K562	blood:
2	chr1:77813619..77816574-chr1:78468319..78470340,2	K562	blood:
3	chr1:45195514..45197967-chr1:78468300..78470449,2	K562	blood:
4	chr1:78469181..78471632-chr1:85154975..85157700,2	K562	blood:
5	chr1:78468129..78475881-chr1:78555411..78565499,18	K562	blood:
6	chr1:78469483..78470465-chr1:159894832..159895503,2	Hela-S3	cervix:
7	chr1:78468848..78471469-chr13:91999787..92002475,2	K562	blood:
8	chr1:78354412..78357543-chr1:78468778..78471529,4	K562	blood:
9	chr1:78470014..78470820-chr19:11485458..11486026,2	HCT-116	colon:
10	chr1:78469772..78470679-chr6:26271386..26272299,2	Hela-S3	cervix:
11	chr1:78147072..78148946-chr1:78468394..78471551,4	K562	blood:
12	chr1:78223538..78227787-chr1:78468626..78471641,9	K562	blood:
13	chr1:78469811..78470546-chr17:56736091..56736667,2	HCT-116	colon:
14	chr1:36273666..36274525-chr1:78469915..78470725,2	Hela-S3	cervix:
15	chr1:78469701..78470650-chr4:10118290..10119096,2	NB4	blood:
16	chr1:78469769..78470335-chr12:123848922..123849686,2	Hela-S3	cervix:
17	chr1:78467305..78472459-chr1:78554681..78560615,12	K562	blood:
18	chr1:78469050..78471034-chr12:6647228..6648916,2	K562	blood:
19	chr1:78148235..78150616-chr1:78467949..78471468,6	K562	blood:
20	chr1:78468722..78470321-chr1:110881687..110883282,2	K562	blood:
21	chr1:78466099..78472038-chr1:78511575..78517585,8	K562	blood:
22	chr1:78469679..78470448-chr11:62608476..62609646,4	Hela-S3	cervix:
23	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
24	chr1:78470006..78470576-chrX:71400976..71401889,2	Hela-S3	cervix:
25	chr1:78469598..78470450-chr15:66648596..66649216,2	Hela-S3	cervix:
26	chr1:78469748..78470406-chr19:35168106..35168785,2	HCT-116	colon:
27	chr1:78469811..78470339-chr2:64067570..64068396,2	Hela-S3	cervix:
28	chr1:78469866..78470559-chr9:6757407..6758029,2	NB4	blood:
29	chr1:78469750..78470464-chr14:75745248..75745748,2	Hela-S3	cervix:
30	chr1:78469893..78470576-chr9:74383453..74384115,2	Hela-S3	cervix:
31	chr1:78469798..78470602-chr6:16128942..16129625,2	Hela-S3	cervix:
32	chr1:67895339..67897749-chr1:78469184..78471380,2	K562	blood:
33	chr1:78444790..78445968-chr1:78469428..78470562,4	Hela-S3	cervix:
34	chr1:78469578..78470998-chr12:52444680..52445780,5	Hela-S3	cervix:
35	chr1:78470170..78473101-chr7:44834709..44837189,2	K562	blood:
36	chr1:78469979..78470530-chr17:76311568..76312104,2	Hela-S3	cervix:
37	chr1:78148970..78151388-chr1:78468544..78472172,4	K562	blood:
38	chr1:78470112..78470655-chr3:50365403..50366265,2	Hela-S3	cervix:
39	chr1:78441980..78446801-chr1:78467462..78471771,12	MCF-7	breast:
40	chr1:78469894..78470597-chr6:111302819..111303506,2	Hela-S3	cervix:
41	chr1:78469721..78470513-chr12:49524722..49525238,2	NB4	blood:
42	chr1:78469665..78470320-chr22:43410838..43411749,2	Hela-S3	cervix:
43	chr1:78469755..78470629-chr3:4534572..4535280,2	NB4	blood:
44	chr1:78469796..78470397-chr12:62996212..62997091,2	NB4	blood:
45	chr1:78245266..78247421-chr1:78469203..78472150,2	K562	blood:
46	chr1:76251016..76253217-chr1:78469296..78471512,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273338	TF binding region
DNAJB4	TF binding region
ENSG00000150995	Chromatin interaction
ENSG00000114383	Chromatin interaction
ENSG00000077254	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000197498	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000180488	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000235927	Chromatin interaction
ENSG00000036549	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000100266	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000213560	Chromatin interaction
ENSG00000162775	Chromatin interaction
ENSG00000007944	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000267277	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000196262	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000251958	Chromatin interaction
ENSG00000137960	Chromatin interaction
ENSG00000107077	Chromatin interaction
ENSG00000222849	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000135048	Chromatin interaction
ENSG00000267737	Chromatin interaction
ENSG00000134698	Chromatin interaction
ENSG00000075131	Chromatin interaction
ENSG00000256383	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000231249	Chromatin interaction
ENSG00000089335	Chromatin interaction
ENSG00000269968	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000071127	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000102309	Chromatin interaction
ENSG00000202263	Chromatin interaction
ENSG00000169764	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000233099	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000142864	Chromatin interaction
ENSG00000227963	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17101048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17101052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17101082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[ASN][1000 genomes]
rs17101109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2228247	0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2296455	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[ASN][1000 genomes]
rs28362659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34128192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3767027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56325960	0.93[EUR][1000 genomes]
rs59087988	0.91[ASN][1000 genomes]
rs72685391	1.00[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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv1801396	chr1:78468094-78492221	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28362660	FUBP1	cis	lymphoblastoid	seeQTL
rs28362660	NEXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78446600-78470400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:78448800-78488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:78452800-78470400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:78452800-78478800	Weak transcription	Spleen	Spleen
5	chr1:78454200-78485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:78456200-78470400	Weak transcription	Esophagus	oesophagus
7	chr1:78457400-78470400	Weak transcription	Pancreas	Pancrea
8	chr1:78461400-78470800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:78468200-78473600	Active TSS	A549	lung
10	chr1:78468400-78475800	Active TSS	Right Atrium	heart
11	chr1:78468600-78473400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr1:78468600-78475000	Active TSS	K562	blood
13	chr1:78469000-78470400	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr1:78469000-78471000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:78469000-78472000	Active TSS	Primary monocytes fromperipheralblood	blood
16	chr1:78469000-78473400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:78469200-78471800	Active TSS	HSMM	muscle
18	chr1:78469200-78472600	Active TSS	HMEC	breast
19	chr1:78469200-78473400	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:78469200-78473600	Active TSS	Brain Substantia Nigra	brain
21	chr1:78469200-78475400	Active TSS	NHLF	lung
22	chr1:78469400-78471800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:78469400-78472200	Active TSS	Rectal Smooth Muscle	rectum
24	chr1:78469400-78475400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr1:78469600-78471800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:78469600-78471800	Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:78469600-78472200	Active TSS	Adipose Nuclei	Adipose
28	chr1:78469600-78472600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:78469600-78472600	Active TSS	Fetal Stomach	stomach
30	chr1:78469600-78472600	Active TSS	Thymus	Thymus
31	chr1:78469600-78472800	Active TSS	Placenta	Placenta
32	chr1:78469600-78473000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:78469600-78473000	Active TSS	Fetal Intestine Large	intestine
34	chr1:78469600-78473400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:78469600-78473400	Active TSS	GM12878-XiMat	blood
36	chr1:78469600-78473400	Active TSS	Osteobl	bone
37	chr1:78469600-78473600	Active TSS	Brain Hippocampus Middle	brain
38	chr1:78469600-78474400	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr1:78469600-78476400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:78469600-78476800	Active TSS	HSMMtube	muscle
41	chr1:78469600-78477200	Active TSS	Aorta	Aorta
42	chr1:78469800-78471000	Active TSS	Primary T cells from cord blood	blood
43	chr1:78469800-78471000	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:78469800-78471200	Active TSS	Primary hematopoietic stem cells	blood
45	chr1:78469800-78471200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:78469800-78471400	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:78469800-78471400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:78469800-78471400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:78469800-78471400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:78469800-78471600	Active TSS	Primary B cells from peripheral blood	blood

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