Variant report

Variant	rs7146599
Chromosome Location	chr14:24527672-24527673
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	CTCF	chr14:24527600-24527750	AoAF	blood vessel:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
2	CTCF	chr14:24527600-24527750	HUVEC	blood vessel:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
3	CTCF	chr14:24527580-24527730	AoAF	blood vessel:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
4	RAD21	chr14:24527384-24527919	ECC-1	luminal epithelium:	n/a	chr14:24527661-24527680 chr14:24527666-24527676 chr14:24527664-24527677 chr14:24527665-24527674
5	CTCF	chr14:24527483-24527782	A549	lung:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
6	CTCF	chr14:24527600-24527750	SK-N-SH_RA	brain:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
7	CTCF	chr14:24527228-24528028	HCT-116	colon:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
8	CTCF	chr14:24527545-24527826	GM19239	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
9	RAD21	chr14:24527489-24527848	K562	blood:	n/a	chr14:24527661-24527680 chr14:24527666-24527676 chr14:24527664-24527677 chr14:24527665-24527674
10	CTCF	chr14:24527533-24527785	Fibrobl	skin:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
11	MAZ	chr14:24527578-24527834	GM12878	blood:	n/a	n/a
12	CTCF	chr14:24527580-24527730	GM12869	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
13	CTCF	chr14:24527600-24527750	GM12870	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
14	EBF1	chr14:24527635-24527776	GM12878	blood:	n/a	n/a
15	CTCF	chr14:24527600-24527750	HRPEpiC	eye:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
16	CTCF	chr14:24527560-24527752	A549	lung:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
17	REST	chr14:24527492-24527866	A549	lung:	n/a	n/a
18	CTCF	chr14:24527660-24527810	GM12878	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
19	CTCF	chr14:24527469-24527843	K562	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
20	CTCF	chr14:24527529-24527801	Gliobla	brain:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
21	MYBL2	chr14:24527258-24527987	HepG2	liver:	n/a	n/a
22	CHD2	chr14:24527509-24527810	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr14:24527101-24528598	SK-N-SH	brain:	n/a	chr14:24528079-24528091 chr14:24527661-24527680 chr14:24527666-24527676 chr14:24527664-24527677 chr14:24527665-24527674
24	CTCF	chr14:24527620-24527770	HRE	kidney:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
25	CTCF	chr14:24527620-24527770	MCF-7	breast:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
26	CTCF	chr14:24527580-24527730	GM12871	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
27	CTCF	chr14:24527580-24527730	HUVEC	blood vessel:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
28	CTCF	chr14:24527524-24527827	ECC-1	luminal epithelium:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
29	BRCA1	chr14:24527622-24527739	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr14:24527539-24527796	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr14:24527561-24527787	MCF-7	breast:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
32	RAD21	chr14:24527341-24527992	MCF-7	breast:	n/a	chr14:24527661-24527680 chr14:24527666-24527676 chr14:24527664-24527677 chr14:24527665-24527674
33	CTCF	chr14:24527600-24527750	GM12875	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
34	CTCF	chr14:24527526-24527808	MCF-7	breast:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
35	CTCF	chr14:24527620-24527770	GM12868	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
36	CTCF	chr14:24527547-24527786	MCF-7	breast:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
37	CTCF	chr14:24527428-24527819	HepG2	liver:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
38	CTCF	chr14:24527620-24527770	GM12874	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
39	RCOR1	chr14:24527558-24527810	HepG2	liver:	n/a	n/a
40	CTCF	chr14:24527577-24527770	H1-hESC	embryonic stem cell:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
41	MAFK	chr14:24527522-24527697	K562	blood:	n/a	n/a
42	CTCF	chr14:24527518-24527855	T-47D	breast:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
43	CTCF	chr14:24527580-24527730	GM06990	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
44	ZMIZ1	chr14:24527587-24527783	K562	blood:	n/a	n/a
45	CTCF	chr14:24527580-24527730	GM12864	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
46	CTCF	chr14:24527560-24527710	GM12873	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
47	CTCF	chr14:24527600-24527750	HBMEC	blood vessel:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
48	RCOR1	chr14:24527574-24527777	K562	blood:	n/a	n/a
49	CTCF	chr14:24527600-24527750	BJ	skin:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672
50	CTCF	chr14:24527600-24527750	GM12867	blood:	n/a	chr14:24527662-24527683 chr14:24527665-24527675 chr14:24527663-24527676 chr14:24527660-24527678 chr14:24527663-24527672

No.	Distal block	Cell Line	Cell type
1	chr14:24527305..24528103-chr14:24577802..24578457,2	MCF-7	breast:
2	chr14:24526433..24530334-chr14:24563337..24565125,5	K562	blood:
3	chr14:24527264..24528168-chr14:24766160..24766741,2	K562	blood:
4	chr14:24526871..24528812-chr14:24546402..24548795,2	MCF-7	breast:
5	chr14:24527244..24528161-chr14:24559819..24560368,5	K562	blood:
6	chr14:24526634..24530283-chr14:24563210..24565999,4	MCF-7	breast:
7	chr14:24527348..24529329-chr14:24572772..24574744,2	K562	blood:
8	chr14:24527104..24528114-chr14:24577764..24578949,8	MCF-7	breast:
9	chr14:24527119..24528160-chr14:24577459..24578694,4	K562	blood:
10	chr14:24523011..24525249-chr14:24526454..24529124,3	K562	blood:
11	chr14:24526765..24529222-chr14:24603815..24606214,2	MCF-7	breast:
12	chr14:24527087..24529685-chr14:24531747..24536004,3	K562	blood:
13	chr14:24527144..24528521-chr14:24559426..24560661,30	MCF-7	breast:
14	chr14:24527263..24528098-chr14:24766176..24766963,2	MCF-7	breast:
15	chr14:24526616..24529222-chr14:24536297..24538563,2	MCF-7	breast:
16	chr14:24525339..24528108-chr14:24566974..24569248,2	MCF-7	breast:
17	chr14:24527208..24528646-chr14:24559174..24560390,16	MCF-7	breast:
18	chr14:24526357..24527984-chr14:24640632..24642546,2	MCF-7	breast:

Variant related genes	Relation type
LRRC16B	TF binding region
ENSG00000092010	Chromatin interaction
ENSG00000129535	Chromatin interaction
ENSG00000100889	Chromatin interaction
ENSG00000100918	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10132601	1.00[CHB][hapmap]
rs11158525	0.82[GIH][hapmap]
rs11574512	1.00[CHB][hapmap]
rs11622481	1.00[CHB][hapmap]
rs11626841	0.81[CEU][hapmap]
rs17101262	1.00[CHB][hapmap]
rs17101962	1.00[CHB][hapmap]
rs2229464	1.00[CHB][hapmap]
rs2229660	1.00[CHB][hapmap]
rs2855009	1.00[CHB][hapmap]
rs7152726	0.81[CEU][hapmap]
rs8017358	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405661	chr14:24189883-24670942	Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv1049316	chr14:24405420-24583724	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv541999	chr14:24405420-24583724	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv1052180	chr14:24429298-24555710	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv516023	chr14:24489605-24550224	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1036658	chr14:24513905-24555710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv1827678	chr14:24520544-24663325	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv456168	chr14:24525634-24618859	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	90 gene(s)	inside rSNPs	diseases
9	nsv564057	chr14:24525634-24618859	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription 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	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7146599	LRRC16B	cis	cerebellum	SCAN
rs7146599	SAG	trans	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24522200-24527800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:24522200-24528000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr14:24522200-24529000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:24522200-24529200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr14:24522200-24539400	Weak transcription	Right Atrium	heart
6	chr14:24522200-24541000	Weak transcription	Spleen	Spleen
7	chr14:24522200-24547200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr14:24522200-24549400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:24522400-24534600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr14:24522400-24540000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr14:24523000-24529000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr14:24523000-24539600	Weak transcription	Brain Angular Gyrus	brain
13	chr14:24523000-24540800	Weak transcription	Brain Hippocampus Middle	brain
14	chr14:24523200-24527800	Weak transcription	Fetal Intestine Small	intestine
15	chr14:24523200-24534200	Strong transcription	Brain Germinal Matrix	brain
16	chr14:24523200-24536200	Weak transcription	Brain Substantia Nigra	brain
17	chr14:24523200-24537400	Strong transcription	Fetal Brain Female	brain
18	chr14:24523200-24541200	Weak transcription	Esophagus	oesophagus
19	chr14:24525000-24540200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:24525200-24539600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:24525400-24529800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr14:24525800-24534600	Enhancers	Liver	Liver
23	chr14:24526200-24533600	Enhancers	Duodenum Mucosa	Duodenum
24	chr14:24527000-24528000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr14:24527400-24528000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:24527400-24528000	Enhancers	Fetal Brain Male	brain
27	chr14:24527400-24528000	Enhancers	Fetal Thymus	thymus
28	chr14:24527400-24528000	Enhancers	Gastric	stomach
29	chr14:24527400-24528000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr14:24527400-24533000	Enhancers	Fetal Intestine Large	intestine
31	chr14:24527600-24527800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr14:24527600-24527800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr14:24527600-24527800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr14:24527600-24528000	Enhancers	Brain Anterior Caudate	brain
35	chr14:24527600-24528000	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr14:24527600-24528600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:24527600-24528600	Enhancers	Fetal Muscle Leg	muscle
38	chr14:24527600-24528600	Bivalent Enhancer	HepG2	liver

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