Variant report

Variant	rs7644995
Chromosome Location	chr3:46530169-46530170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:123)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:123 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZEB1	chr3:46530165-46530618	GM12878	blood:	n/a	n/a
2	JUND	chr3:46530147-46530611	K562	blood:	n/a	n/a
3	RAD21	chr3:46530129-46530661	ECC-1	luminal epithelium:	n/a	n/a
4	RCOR1	chr3:46530162-46530780	Hela-S3	cervix:	n/a	n/a
5	MYC	chr3:46530156-46530625	K562	blood:	n/a	n/a
6	TEAD4	chr3:46530091-46530611	K562	blood:	n/a	n/a
7	ATF2	chr3:46530151-46530620	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:46530139-46530880	H1-hESC	embryonic stem cell:	n/a	n/a
9	RUNX3	chr3:46530159-46530646	GM12878	blood:	n/a	n/a
10	EP300	chr3:46530164-46530578	K562	blood:	n/a	n/a
11	MAX	chr3:46530164-46530801	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr3:46530064-46530663	A549	lung:	n/a	n/a
13	RAD21	chr3:46530153-46530617	K562	blood:	n/a	n/a
14	TCF3	chr3:46530161-46530588	GM12878	blood:	n/a	n/a
15	BCLAF1	chr3:46530133-46530574	GM12878	blood:	n/a	n/a
16	RAD21	chr3:46530125-46530768	IMR90	lung:	n/a	n/a
17	MAZ	chr3:46530157-46530637	K562	blood:	n/a	n/a
18	CHD1	chr3:46530077-46530738	IMR90	lung:	n/a	n/a
19	ZC3H11A	chr3:46530159-46530607	K562	blood:	n/a	n/a
20	YY1	chr3:46530148-46530589	H1-hESC	embryonic stem cell:	n/a	n/a
21	ATF2	chr3:46530160-46530603	H1-hESC	embryonic stem cell:	n/a	n/a
22	TEAD4	chr3:46530093-46530734	K562	blood:	n/a	n/a
23	RAD21	chr3:46530090-46530808	ECC-1	luminal epithelium:	n/a	n/a
24	RUNX3	chr3:46530131-46530682	GM12878	blood:	n/a	n/a
25	CBX3	chr3:46530128-46530656	K562	blood:	n/a	n/a
26	RCOR1	chr3:46530155-46530827	IMR90	lung:	n/a	n/a
27	CTCF	chr3:46530122-46530578	A549	lung:	n/a	n/a
28	CTCF	chr3:46530072-46530691	H1-hESC	embryonic stem cell:	n/a	n/a
29	SMC3	chr3:46530143-46530721	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr3:46530108-46530635	K562	blood:	n/a	n/a
31	IRF4	chr3:46530142-46530574	GM12878	blood:	n/a	n/a
32	RXRA	chr3:46530122-46530725	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr3:46530109-46530696	H1-hESC	embryonic stem cell:	n/a	n/a
34	SMC3	chr3:46530148-46530535	HepG2	liver:	n/a	n/a
35	MAX	chr3:46530073-46530696	A549	lung:	n/a	n/a
36	CTCF	chr3:46530121-46530847	IMR90	lung:	n/a	n/a
37	FOXM1	chr3:46530104-46530670	GM12878	blood:	n/a	n/a
38	MAFK	chr3:46530159-46530618	K562	blood:	n/a	n/a
39	MYC	chr3:46530156-46530806	NB4	blood:	n/a	n/a
40	CTCF	chr3:46530134-46530579	A549	lung:	n/a	n/a
41	RAD21	chr3:46530161-46530522	GM12878	blood:	n/a	n/a
42	CTCF	chr3:46530043-46531002	A549	lung:	n/a	n/a
43	MAX	chr3:46530109-46530618	A549	lung:	n/a	n/a
44	RAD21	chr3:46530056-46530873	HCT-116	colon:	n/a	n/a
45	CTCF	chr3:46530080-46530633	HepG2	liver:	n/a	n/a
46	RAD21	chr3:46530109-46530703	H1-hESC	embryonic stem cell:	n/a	n/a
47	E2F6	chr3:46530149-46530940	H1-hESC	embryonic stem cell:	n/a	n/a
48	ZNF143	chr3:46530144-46530586	K562	blood:	n/a	n/a
49	SMC3	chr3:46530066-46530770	SK-N-SH	brain:	n/a	n/a
50	SMC3	chr3:46530129-46530745	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46529857..46530830-chr3:46549274..46550154,2	K562	blood:
2	chr3:46529862..46530377-chr3:64516333..64517197,2	MCF-7	breast:
3	chr2:233835955..233836476-chr3:46529913..46530430,3	MCF-7	breast:
4	chr3:46529878..46530429-chr3:46671116..46672037,3	MCF-7	breast:
5	chr1:121484254..121485268-chr3:46529887..46530781,3	MCF-7	breast:
6	chr3:46441887..46442673-chr3:46529916..46530717,2	K562	blood:
7	chr3:46490983..46491780-chr3:46529871..46530687,2	MCF-7	breast:
8	chr3:46529979..46530787-chr3:46607787..46608328,2	K562	blood:
9	chr3:46529944..46530794-chr3:46705110..46706015,2	K562	blood:
10	chr3:46529686..46530942-chr3:46599020..46600485,46	MCF-7	breast:
11	chr3:46528809..46531447-chr3:46546904..46549677,2	K562	blood:
12	chr3:46529871..46530872-chr3:46670590..46672462,23	K562	blood:
13	chr2:171671918..171672781-chr3:46529676..46530675,2	MCF-7	breast:
14	chr3:46529825..46532011-chr3:46599266..46600570,56	K562	blood:
15	chr3:46529884..46530839-chr3:46671105..46672532,19	MCF-7	breast:
16	chr3:46529889..46530997-chr3:46599244..46600312,18	MCF-7	breast:
17	chr3:46529904..46530772-chr3:46603076..46604060,2	K562	blood:

No data

Variant related genes	Relation type
LTF	TF binding region
ENSG00000163827	Chromatin interaction
ENSG00000128683	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11716682	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11919651	1.00[CHB][hapmap]
rs11929118	1.00[YRI][hapmap]
rs12639258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13084167	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327723	1.00[CHB][hapmap]
rs4637321	0.84[EUR][1000 genomes]
rs6414427	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414428	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6441999	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7371865	1.00[ASW][hapmap]
rs7374925	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7641783	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46511800-46530200	Weak transcription	Right Atrium	heart
2	chr3:46522800-46530200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:46522800-46530400	Weak transcription	Gastric	stomach
4	chr3:46524800-46530400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:46525000-46530600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:46525800-46530400	Weak transcription	Right Ventricle	heart
7	chr3:46526200-46530200	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:46526800-46530400	Weak transcription	Spleen	Spleen
9	chr3:46527000-46530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:46527200-46530200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:46527200-46530200	Weak transcription	Placenta	Placenta
12	chr3:46527200-46530400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:46527200-46530400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:46527400-46530200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:46527400-46530400	Weak transcription	Pancreas	Pancrea
16	chr3:46527400-46530400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:46527400-46530400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:46527400-46530400	Weak transcription	Stomach Mucosa	stomach
19	chr3:46527400-46530400	Weak transcription	HSMM	muscle
20	chr3:46527400-46530600	Weak transcription	HSMMtube	muscle
21	chr3:46527600-46530200	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:46527600-46530400	Weak transcription	HepG2	liver
23	chr3:46527800-46530400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:46528400-46530200	Weak transcription	Fetal Intestine Large	intestine
25	chr3:46529400-46534200	Enhancers	Dnd41	blood
26	chr3:46529600-46530400	Weak transcription	Brain Substantia Nigra	brain
27	chr3:46529800-46531200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr3:46530000-46530200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:46530000-46530400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:46530000-46530400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:46530000-46530400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:46530000-46531000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:46530000-46531600	Enhancers	Fetal Thymus	thymus
34	chr3:46530000-46531800	Enhancers	NH-A	brain

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