Variant report

Variant	rs4999690
Chromosome Location	chr16:74778006-74778007
allele	A/G
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	GATA3	chr16:74777460-74778238	A549	lung:	n/a	n/a
2	FOXA1	chr16:74777847-74778171	T-47D	breast:	n/a	n/a
3	FOSL2	chr16:74777456-74778264	A549	lung:	n/a	chr16:74778028-74778042
4	MAZ	chr16:74777270-74778511	IMR90	lung:	n/a	chr16:74777788-74777795
5	GTF2F1	chr16:74777295-74778235	Hela-S3	cervix:	n/a	n/a
6	USF1	chr16:74777556-74778188	A549	lung:	n/a	n/a
7	MAX	chr16:74777405-74778335	MCF-7	breast:	n/a	chr16:74777788-74777795
8	BHLHE40	chr16:74777768-74778135	HepG2	liver:	n/a	n/a
9	FOS	chr16:74777519-74778274	MCF10A-Er-Src	breast:	n/a	chr16:74778028-74778042
10	ETS1	chr16:74777559-74778258	A549	lung:	n/a	chr16:74777972-74777986
11	HDAC2	chr16:74777469-74778274	MCF-7	breast:	n/a	n/a
12	KAP1	chr16:74777104-74778273	U2OS	brain:	n/a	n/a
13	GABPA	chr16:74777391-74778286	A549	lung:	n/a	n/a
14	STAT3	chr16:74777522-74778300	MCF10A-Er-Src	breast:	n/a	chr16:74778187-74778201 chr16:74778188-74778199
15	REST	chr16:74777108-74778373	A549	lung:	n/a	n/a
16	EP300	chr16:74777100-74778447	A549	lung:	n/a	chr16:74777174-74777183
17	BCL3	chr16:74777159-74778431	A549	lung:	n/a	n/a
18	STAT3	chr16:74777566-74778341	MCF10A-Er-Src	breast:	n/a	chr16:74778187-74778201 chr16:74778188-74778199 chr16:74778306-74778317
19	SIN3AK20	chr16:74777442-74778179	A549	lung:	n/a	n/a
20	FOS	chr16:74777565-74778274	MCF10A-Er-Src	breast:	n/a	chr16:74778028-74778042
21	MYC	chr16:74777525-74778271	MCF10A-Er-Src	breast:	n/a	chr16:74777788-74777795
22	TEAD4	chr16:74777331-74778306	A549	lung:	n/a	n/a
23	ZBTB33	chr16:74777778-74778234	A549	lung:	n/a	n/a
24	MYC	chr16:74777929-74778060	MCF-7	breast:	n/a	n/a
25	RCOR1	chr16:74777921-74778102	HepG2	liver:	n/a	n/a
26	SP1	chr16:74777118-74778383	A549	lung:	n/a	chr16:74777372-74777386 chr16:74777692-74777702 chr16:74777483-74777497
27	CEBPB	chr16:74777169-74778122	A549	lung:	n/a	n/a
28	MAX	chr16:74777045-74778417	A549	lung:	n/a	chr16:74777788-74777795
29	FOXA2	chr16:74777927-74778199	HepG2	liver:	n/a	n/a
30	POLR2A	chr16:74777340-74778204	Hela-S3	cervix:	n/a	n/a
31	SIX5	chr16:74776917-74778350	A549	lung:	n/a	n/a
32	MYC	chr16:74777998-74778073	HepG2	liver:	n/a	n/a
33	GATA3	chr16:74777417-74778336	MCF-7	breast:	n/a	n/a
34	POLR2A	chr16:74777282-74778145	HCT-116	colon:	n/a	n/a
35	POLR2A	chr16:74777437-74778192	HCT-116	colon:	n/a	n/a
36	MAX	chr16:74777836-74778140	HepG2	liver:	n/a	n/a
37	ZBTB33	chr16:74777470-74778210	A549	lung:	n/a	n/a
38	MAX	chr16:74777077-74778248	A549	lung:	n/a	chr16:74777788-74777795
39	SP1	chr16:74777043-74778456	A549	lung:	n/a	chr16:74777372-74777386 chr16:74777692-74777702 chr16:74777483-74777497
40	NR2F2	chr16:74777251-74778399	MCF-7	breast:	n/a	n/a
41	JUND	chr16:74777389-74778321	A549	lung:	n/a	chr16:74778028-74778042
42	SP1	chr16:74777218-74778492	HCT-116	colon:	n/a	chr16:74777372-74777386 chr16:74777692-74777702 chr16:74777483-74777497
43	TCF12	chr16:74776877-74778460	A549	lung:	n/a	n/a
44	POLR2A	chr16:74777152-74778242	Hela-S3	cervix:	n/a	n/a
45	ATF3	chr16:74777371-74778188	A549	lung:	n/a	n/a
46	TEAD4	chr16:74777539-74778302	A549	lung:	n/a	n/a
47	RFX5	chr16:74777367-74778256	Hela-S3	cervix:	n/a	n/a
48	RFX5	chr16:74777601-74778149	HepG2	liver:	n/a	n/a
49	MYC	chr16:74777427-74778224	MCF10A-Er-Src	breast:	n/a	chr16:74777788-74777795
50	NR3C1	chr16:74777426-74778316	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:74777335..74778147-chr17:15902566..15903225,2	Hela-S3	cervix:
2	chr16:74776402..74778340-chr16:74807452..74809471,3	MCF-7	breast:
3	chr16:74777555..74778238-chr9:127623848..127624403,2	Hela-S3	cervix:
4	chr16:74771379..74775079-chr16:74776185..74779288,5	MCF-7	breast:
5	chr16:74761154..74764100-chr16:74775232..74779414,3	MCF-7	breast:
6	chr16:74774896..74778280-chr16:74780880..74783972,4	MCF-7	breast:
7	chr16:74777526..74778487-chrX:40439750..40440648,2	Hela-S3	cervix:
8	chr1:179850736..179851572-chr16:74777514..74778347,2	Hela-S3	cervix:
9	chr1:150550125..150550878-chr16:74777507..74778055,2	Hela-S3	cervix:
10	chr16:74758826..74760555-chr16:74776363..74778066,2	MCF-7	breast:
11	chr10:74032873..74033584-chr16:74777424..74778272,2	Hela-S3	cervix:
12	chr16:74767389..74769138-chr16:74776041..74778076,3	MCF-7	breast:
13	chr16:74777433..74778084-chr17:80186307..80187183,2	Hela-S3	cervix:
14	chr16:74770638..74773504-chr16:74776084..74778878,2	MCF-7	breast:
15	chr11:42247914..42248414-chr16:74777515..74778120,2	Hela-S3	cervix:
16	chr10:75504092..75504955-chr16:74777288..74778124,2	Hela-S3	cervix:
17	chr16:74776670..74778325-chr16:74825390..74827432,2	MCF-7	breast:
18	chr16:74777620..74778145-chr6:26123992..26124825,2	Hela-S3	cervix:
19	chr15:65596810..65597751-chr16:74777460..74778250,2	Hela-S3	cervix:
20	chr1:156470670..156471273-chr16:74777160..74778024,2	Hela-S3	cervix:
21	chr16:74777082..74778287-chr16:74807922..74809140,6	Hela-S3	cervix:
22	chr12:52540731..52541610-chr16:74777345..74778111,2	Hela-S3	cervix:
23	chr15:93448661..93449558-chr16:74777222..74778009,2	Hela-S3	cervix:
24	chr16:74777177..74778082-chr7:75676774..75677380,2	Hela-S3	cervix:
25	chr12:80084666..80085260-chr16:74777626..74778238,2	Hela-S3	cervix:
26	chr16:74765764..74767336-chr16:74777877..74779461,2	MCF-7	breast:

Variant related genes	Relation type
FA2H	TF binding region
ENSG00000263661	TF binding region
ENSG00000182220	Chromatin interaction
ENSG00000127952	Chromatin interaction
ENSG00000141526	Chromatin interaction
ENSG00000103089	Chromatin interaction
ENSG00000136942	Chromatin interaction
ENSG00000263661	Chromatin interaction
ENSG00000176986	Chromatin interaction
ENSG00000146701	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000177425	Chromatin interaction
ENSG00000011295	Chromatin interaction
ENSG00000214941	Chromatin interaction
ENSG00000200156	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11643479	0.83[ASW][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2240251	0.81[CEU][hapmap]
rs2240253	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs241368	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs241376	0.87[ASN][1000 genomes]
rs241377	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv906907	chr16:74702254-74785902	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv517513	chr16:74743736-74812676	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
10	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
13	nsv457520	chr16:74758984-74907440	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv572976	chr16:74758984-74907440	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4999690	SNTB2	cis	cerebellum	SCAN
rs4999690	MON1B	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74763200-74779000	Weak transcription	Right Atrium	heart
2	chr16:74764000-74781800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr16:74769200-74783200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr16:74769400-74782800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr16:74772400-74783400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr16:74774000-74781800	Enhancers	Brain Hippocampus Middle	brain
7	chr16:74775000-74782800	Weak transcription	Esophagus	oesophagus
8	chr16:74775200-74778200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr16:74775200-74779000	Enhancers	Stomach Mucosa	stomach
10	chr16:74775200-74784800	Enhancers	Brain Substantia Nigra	brain
11	chr16:74775400-74782000	Enhancers	Brain Cingulate Gyrus	brain
12	chr16:74776200-74783600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr16:74776400-74778800	Weak transcription	Gastric	stomach
14	chr16:74776400-74782000	Enhancers	Brain Angular Gyrus	brain
15	chr16:74776800-74778200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr16:74776800-74779600	Enhancers	HMEC	breast
17	chr16:74776800-74782000	Enhancers	Brain Anterior Caudate	brain
18	chr16:74777000-74778400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr16:74777000-74778400	Flanking Active TSS	Hela-S3	cervix
20	chr16:74777200-74778200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr16:74777200-74778200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:74777200-74778200	Enhancers	Placenta	Placenta
23	chr16:74777200-74778200	Enhancers	NH-A	brain
24	chr16:74777200-74778200	Flanking Active TSS	NHEK	skin
25	chr16:74777200-74778400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:74777400-74778200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr16:74777400-74778200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:74777400-74778200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr16:74777400-74778200	Flanking Bivalent TSS/Enh	HepG2	liver
30	chr16:74777400-74778400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr16:74777400-74778400	Enhancers	Colon Smooth Muscle	Colon
32	chr16:74777400-74778600	Enhancers	NHLF	lung
33	chr16:74777400-74779600	Enhancers	Pancreas	Pancrea
34	chr16:74777600-74778200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr16:74777600-74778200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr16:74777600-74778200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr16:74777600-74778800	Enhancers	Fetal Intestine Small	intestine
38	chr16:74777600-74779000	Weak transcription	GM12878-XiMat	blood
39	chr16:74777600-74780000	Enhancers	Fetal Intestine Large	intestine
40	chr16:74777600-74781400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr16:74777600-74783200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:74777600-74802400	Weak transcription	Thymus	Thymus
43	chr16:74777800-74781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr16:74777800-74781800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr16:74777800-74781800	Weak transcription	Fetal Thymus	thymus
46	chr16:74777800-74782800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr16:74777800-74783000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr16:74778000-74778200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr16:74778000-74778200	Enhancers	K562	blood
50	chr16:74778000-74778400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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