Variant report

Variant	rs56723304
Chromosome Location	chr6:150328304-150328305
allele	C/T
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	chr6:150328300-150328450	GM12871	blood:	n/a	chr6:150328436-150328449 chr6:150328436-150328445
2	CTCF	chr6:150328300-150328450	GM12865	blood:	n/a	chr6:150328436-150328449 chr6:150328436-150328445
3	CTCF	chr6:150328300-150328450	GM12864	blood:	n/a	chr6:150328436-150328449 chr6:150328436-150328445
4	RAD21	chr6:150328206-150328643	H1-hESC	embryonic stem cell:	n/a	chr6:150328444-150328463
5	CTCF	chr6:150328253-150328632	IMR90	lung:	n/a	chr6:150328445-150328466 chr6:150328436-150328449 chr6:150328443-150328461 chr6:150328436-150328445
6	CTCF	chr6:150328254-150328558	K562	blood:	n/a	chr6:150328445-150328466 chr6:150328436-150328449 chr6:150328443-150328461 chr6:150328436-150328445
7	CTCF	chr6:150328300-150328450	A549	lung:	n/a	chr6:150328436-150328449 chr6:150328436-150328445
8	CTCF	chr6:150328300-150328450	GM12878	blood:	n/a	chr6:150328436-150328449 chr6:150328436-150328445
9	TCF12	chr6:150328141-150328481	GM12878	blood:	n/a	chr6:150328411-150328421
10	BATF	chr6:150328171-150328476	GM12878	blood:	n/a	n/a
11	RAD21	chr6:150328224-150328495	GM12878	blood:	n/a	chr6:150328444-150328463
12	CTCF	chr6:150328302-150328570	K562	blood:	n/a	chr6:150328445-150328466 chr6:150328436-150328449 chr6:150328443-150328461 chr6:150328436-150328445
13	RAD21	chr6:150328261-150328608	H1-hESC	embryonic stem cell:	n/a	chr6:150328444-150328463
14	YY1	chr6:150328121-150328493	GM12878	blood:	n/a	n/a
15	RAD21	chr6:150328279-150328607	IMR90	lung:	n/a	chr6:150328444-150328463
16	RAD21	chr6:150328284-150328614	Hela-S3	cervix:	n/a	chr6:150328444-150328463
17	CEBPB	chr6:150328064-150328586	GM12878	blood:	n/a	n/a
18	SMC3	chr6:150328269-150328461	K562	blood:	n/a	chr6:150328445-150328459
19	CTCF	chr6:150328281-150328499	A549	lung:	n/a	chr6:150328445-150328466 chr6:150328436-150328449 chr6:150328443-150328461 chr6:150328436-150328445
20	CTCF	chr6:150328237-150328629	GM12878	blood:	n/a	chr6:150328445-150328466 chr6:150328436-150328449 chr6:150328443-150328461 chr6:150328436-150328445
21	CTCF	chr6:150328242-150328623	K562	blood:	n/a	chr6:150328445-150328466 chr6:150328436-150328449 chr6:150328443-150328461 chr6:150328436-150328445
22	CTCF	chr6:150328300-150328450	Caco-2	colon:	n/a	chr6:150328436-150328449 chr6:150328436-150328445
23	ATF2	chr6:150328002-150328596	GM12878	blood:	n/a	n/a
24	EGR1	chr6:150328097-150328320	GM12878	blood:	n/a	chr6:150328215-150328228 chr6:150328216-150328230 chr6:150328214-150328229
25	RUNX3	chr6:150328079-150328563	GM12878	blood:	n/a	n/a
26	PML	chr6:150328099-150328602	GM12878	blood:	n/a	n/a
27	TBL1XR1	chr6:150328227-150328433	GM12878	blood:	n/a	n/a
28	MAZ	chr6:150328286-150328577	K562	blood:	n/a	n/a
29	SMC3	chr6:150328243-150328515	GM12878	blood:	n/a	chr6:150328445-150328459
30	STAT5A	chr6:150328164-150328499	GM12878	blood:	n/a	chr6:150328226-150328237
31	ZNF143	chr6:150328301-150328604	GM12878	blood:	n/a	n/a
32	RAD21	chr6:150328289-150328529	ECC-1	luminal epithelium:	n/a	chr6:150328444-150328463
33	ZNF384	chr6:150328293-150328600	K562	blood:	n/a	n/a
34	BHLHE40	chr6:150328197-150328464	GM12878	blood:	n/a	n/a
35	BCL11A	chr6:150328061-150328481	GM12878	blood:	n/a	chr6:150328226-150328235 chr6:150328420-150328429
36	MTA3	chr6:150328113-150328570	GM12878	blood:	n/a	n/a
37	NFATC1	chr6:150328144-150328507	GM12878	blood:	n/a	n/a
38	RAD21	chr6:150328235-150328575	A549	lung:	n/a	chr6:150328444-150328463
39	NFATC1	chr6:150328154-150328459	GM12878	blood:	n/a	n/a
40	POU2F2	chr6:150328025-150328465	GM12891	blood:	n/a	n/a
41	BCLAF1	chr6:150328046-150328455	GM12878	blood:	n/a	chr6:150328226-150328235 chr6:150328420-150328429
42	CTCF	chr6:150328160-150328310	NHLF	lung:	n/a	n/a
43	MTA3	chr6:150328104-150328490	GM12878	blood:	n/a	n/a
44	ZNF143	chr6:150328277-150328503	H1-hESC	embryonic stem cell:	n/a	n/a
45	SMC3	chr6:150328275-150328505	Hela-S3	cervix:	n/a	chr6:150328445-150328459
46	RUNX3	chr6:150328044-150328526	GM12878	blood:	n/a	n/a
47	CTCF	chr6:150328300-150328450	K562	blood:	n/a	chr6:150328436-150328449 chr6:150328436-150328445
48	TCF3	chr6:150328116-150328467	GM12878	blood:	n/a	n/a
49	FOXM1	chr6:150328035-150328577	GM12878	blood:	n/a	n/a
50	SP1	chr6:150328130-150328466	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150283785..150286352-chr6:150326807..150328312,2	MCF-7	breast:
2	chr6:150328123..150330822-chr6:150332783..150334807,2	MCF-7	breast:

Variant related genes	Relation type
RAET1K	TF binding region
ENSG00000111981	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11968592	0.98[ASN][1000 genomes]
rs12111470	0.98[ASN][1000 genomes]
rs59880804	0.99[ASN][1000 genomes]
rs61289929	0.99[ASN][1000 genomes]
rs6930447	0.96[ASN][1000 genomes]
rs73779751	0.96[ASN][1000 genomes]
rs73779756	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv970176	chr6:150319173-150343329	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv7375	chr6:150324114-150388625	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3344440	chr6:150324131-150388650	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3323918	chr6:150327978-150392099	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150327000-150328400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr6:150327000-150328400	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr6:150327000-150329600	Weak transcription	HMEC	breast
4	chr6:150327000-150329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:150327200-150329400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:150327200-150329600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:150327200-150329600	Weak transcription	A549	lung
8	chr6:150327400-150328400	Enhancers	Fetal Thymus	thymus
9	chr6:150327400-150329400	Weak transcription	Hela-S3	cervix
10	chr6:150328000-150328400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:150328200-150328400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:150328200-150328400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
13	chr6:150328200-150328400	Enhancers	GM12878-XiMat	blood
14	chr6:150328200-150328400	Enhancers	K562	blood
15	chr6:150328200-150328800	Weak transcription	Lung	lung

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