Variant report

Variant	rs4946979
Chromosome Location	chr6:109805917-109805918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:109805833-109806145	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109804505..109806373-chr6:109808766..109811459,2	K562	blood:
2	chr6:109702597..109705942-chr6:109803330..109806291,3	K562	blood:
3	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
4	chr6:109700978..109703685-chr6:109804896..109807033,2	MCF-7	breast:
5	chr6:109759628..109764398-chr6:109803414..109806709,4	K562	blood:
6	chr6:109804488..109806145-chr6:109811754..109813384,2	K562	blood:

No data

Variant related genes	Relation type
ZBTB24	TF binding region
ENSG00000223537	TF binding region
ENSG00000135535	Chromatin interaction
ENSG00000135587	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000223537	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1476386	0.95[EUR][1000 genomes]
rs1590186	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17602109	0.90[EUR][1000 genomes]
rs2232441	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28635303	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3757232	0.93[EUR][1000 genomes]
rs3757236	0.93[EUR][1000 genomes]
rs4313033	0.95[EUR][1000 genomes]
rs4946969	0.95[EUR][1000 genomes]
rs9480937	0.95[EUR][1000 genomes]
rs9480938	0.95[EUR][1000 genomes]
rs9480959	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9480962	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9480965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9487071	0.95[EUR][1000 genomes]
rs9487077	0.95[EUR][1000 genomes]
rs9487078	0.95[EUR][1000 genomes]
rs9487119	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9487124	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3377564	chr6:109803284-109806132	Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946979	RP11-425D10.10	cis	Thyroid	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109804400-109814200	Weak transcription	Gastric	stomach
2	chr6:109805000-109806600	Weak transcription	Lung	lung
3	chr6:109805000-109817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:109805200-109806000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:109805200-109806000	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:109805200-109806000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr6:109805200-109806200	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:109805200-109806200	Enhancers	HSMM	muscle
9	chr6:109805200-109806800	Enhancers	Fetal Muscle Leg	muscle
10	chr6:109805200-109806800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr6:109805200-109809200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:109805400-109806000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr6:109805400-109806000	Enhancers	Dnd41	blood
14	chr6:109805400-109806000	Enhancers	K562	blood
15	chr6:109805400-109806200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:109805400-109806200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:109805400-109806200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
18	chr6:109805400-109806600	Weak transcription	Fetal Brain Female	brain
19	chr6:109805400-109807200	Weak transcription	A549	lung
20	chr6:109805400-109807200	Weak transcription	Hela-S3	cervix
21	chr6:109805400-109807400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:109805400-109807800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:109805400-109808800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:109805400-109812000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:109805600-109806200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
26	chr6:109805600-109807000	Weak transcription	Stomach Mucosa	stomach
27	chr6:109805600-109807400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:109805600-109812400	Weak transcription	Brain Angular Gyrus	brain
29	chr6:109805800-109806000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr6:109805800-109806000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
31	chr6:109805800-109807000	Weak transcription	Placenta	Placenta

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