Variant report

Variant	rs4907122
Chromosome Location	chr1:85493767-85493768
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:85493334-85493808	A549	lung:	n/a	n/a
2	CTCF	chr1:85493319-85493803	HCT-116	colon:	n/a	n/a
3	CTCF	chr1:85493329-85493829	MCF-7	breast:	n/a	n/a
4	RAD21	chr1:85493291-85493891	HCT-116	colon:	n/a	n/a
5	RAD21	chr1:85493362-85493876	MCF-7	breast:	n/a	n/a
6	CTCF	chr1:85493342-85493812	MCF-7	breast:	n/a	n/a
7	RAD21	chr1:85493400-85493784	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:85493620-85493770	RPTEC	kidney:	n/a	n/a
9	SMC3	chr1:85492931-85493851	GM12878	blood:	n/a	n/a
10	RAD21	chr1:85493079-85493777	GM12878	blood:	n/a	n/a
11	BCLAF1	chr1:85493321-85493825	GM12878	blood:	n/a	n/a
12	RAD21	chr1:85493289-85493889	SK-N-SH	brain:	n/a	n/a
13	YY1	chr1:85493353-85493824	K562	blood:	n/a	n/a
14	RAD21	chr1:85493381-85493812	HCT-116	colon:	n/a	n/a
15	CTCF	chr1:85493317-85493810	GM12878	blood:	n/a	n/a
16	CTCF	chr1:85493269-85493785	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:85409622..85411011-chr1:85492995..85494617,8	MCF-7	breast:
2	chr1:85410272..85411869-chr1:85493014..85494336,19	MCF-7	breast:
3	chr1:85410240..85410751-chr1:85493199..85493798,2	MCF-7	breast:

No data

Variant related genes	Relation type
MCOLN3	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10782535	1.00[ASN][1000 genomes]
rs10873675	1.00[ASN][1000 genomes]
rs1458401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371429	1.00[EUR][1000 genomes]
rs2028304	1.00[YRI][hapmap]
rs2039814	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486647	1.00[ASN][1000 genomes]
rs496561	1.00[ASN][1000 genomes]
rs499579	1.00[ASN][1000 genomes]
rs511765	1.00[ASN][1000 genomes]
rs517156	1.00[ASN][1000 genomes]
rs531169	1.00[ASN][1000 genomes]
rs534908	1.00[ASN][1000 genomes]
rs562126	1.00[ASN][1000 genomes]
rs586403	1.00[ASN][1000 genomes]
rs589227	1.00[ASN][1000 genomes]
rs599137	1.00[ASN][1000 genomes]
rs599888	1.00[ASN][1000 genomes]
rs607298	1.00[ASN][1000 genomes]
rs614194	1.00[ASN][1000 genomes]
rs61769365	1.00[ASN][1000 genomes]
rs641427	1.00[ASN][1000 genomes]
rs6576737	1.00[ASN][1000 genomes]
rs6576740	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6576742	1.00[ASN][1000 genomes]
rs6576743	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664763	1.00[ASN][1000 genomes]
rs6679539	1.00[YRI][hapmap]
rs6684210	1.00[ASN][1000 genomes]
rs679932	1.00[ASN][1000 genomes]
rs680330	1.00[ASN][1000 genomes]
rs7519717	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522239	1.00[YRI][hapmap]
rs7533496	1.00[ASN][1000 genomes]
rs7537692	1.00[ASN][1000 genomes]
rs920340	1.00[ASN][1000 genomes]
rs9804097	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	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 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	chr1:85483600-85494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:85485400-85513000	Weak transcription	Pancreas	Pancrea
3	chr1:85485800-85505200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:85486000-85513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:85486400-85499200	Weak transcription	NHDF-Ad	bronchial
6	chr1:85486400-85500400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:85489000-85500000	Weak transcription	Adipose Nuclei	Adipose
8	chr1:85490800-85494400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:85492200-85497000	Strong transcription	Fetal Intestine Small	intestine
10	chr1:85492800-85493800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:85493000-85495000	Strong transcription	HMEC	breast
12	chr1:85493000-85498200	Strong transcription	Fetal Intestine Large	intestine
13	chr1:85493000-85501000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:85493600-85493800	Enhancers	Osteobl	bone
15	chr1:85493600-85498800	Weak transcription	GM12878-XiMat	blood

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