Variant report

Variant	rs3824883
Chromosome Location	chr11:120172688-120172689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr11:120172432-120173109	MCF-7	breast:	n/a	n/a
2	ESR1	chr11:120172461-120172928	T-47D	breast:	n/a	n/a
3	ZNF217	chr11:120172499-120173117	MCF-7	breast:	n/a	n/a
4	MAX	chr11:120172490-120173233	MCF-7	breast:	n/a	chr11:120172888-120172898 chr11:120172928-120172939
5	NR2F2	chr11:120172426-120173034	MCF-7	breast:	n/a	n/a
6	ESR1	chr11:120172516-120172919	T-47D	breast:	n/a	n/a
7	GATA3	chr11:120172417-120173255	MCF-7	breast:	n/a	n/a
8	ESR1	chr11:120172526-120172947	ECC-1	luminal epithelium:	n/a	n/a
9	ELF1	chr11:120172542-120173321	MCF-7	breast:	n/a	chr11:120173092-120173103
10	MAX	chr11:120172579-120173349	MCF-7	breast:	n/a	chr11:120172888-120172898 chr11:120172928-120172939
11	CEBPB	chr11:120172511-120173117	MCF-7	breast:	n/a	chr11:120172814-120172831
12	FOXA1	chr11:120172522-120173447	T-47D	breast:	n/a	n/a
13	FOXA1	chr11:120172499-120173318	T-47D	breast:	n/a	n/a
14	SIN3AK20	chr11:120172391-120173301	MCF-7	breast:	n/a	n/a
15	GATA3	chr11:120172431-120173179	MCF-7	breast:	n/a	n/a
16	ESR1	chr11:120172475-120172897	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr11:120172595-120172688	MCF-7	breast:	n/a	n/a
18	TCF12	chr11:120172560-120173151	MCF-7	breast:	n/a	n/a
19	ESR1	chr11:120172428-120172937	ECC-1	luminal epithelium:	n/a	n/a
20	ESR1	chr11:120172540-120172990	T-47D	breast:	n/a	n/a
21	EP300	chr11:120172456-120173018	MCF-7	breast:	n/a	n/a
22	HDAC2	chr11:120172614-120173086	MCF-7	breast:	n/a	n/a
23	ELF1	chr11:120172527-120173273	MCF-7	breast:	n/a	chr11:120173092-120173103
24	ESR1	chr11:120172472-120172955	T-47D	breast:	n/a	n/a
25	EP300	chr11:120172459-120173178	T-47D	breast:	n/a	n/a
26	ESR1	chr11:120172508-120172845	ECC-1	luminal epithelium:	n/a	n/a
27	GATA3	chr11:120172410-120173230	T-47D	breast:	n/a	n/a
28	USF1	chr11:120172633-120173128	ECC-1	luminal epithelium:	n/a	n/a
29	ESR1	chr11:120172500-120172866	T-47D	breast:	n/a	n/a
30	GATA3	chr11:120172421-120173247	T-47D	breast:	n/a	n/a
31	MYC	chr11:120172654-120173075	MCF-7	breast:	n/a	chr11:120172888-120172898 chr11:120172928-120172939
32	EP300	chr11:120172483-120173114	T-47D	breast:	n/a	n/a
33	ESR1	chr11:120172532-120172965	ECC-1	luminal epithelium:	n/a	n/a
34	NFIC	chr11:120172619-120173230	ECC-1	luminal epithelium:	n/a	n/a
35	ESR1	chr11:120172577-120172859	ECC-1	luminal epithelium:	n/a	n/a
36	CEBPB	chr11:120172566-120173137	MCF-7	breast:	n/a	chr11:120172814-120172831
37	GATA3	chr11:120172554-120172967	MCF-7	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:120171583..120174537-chr11:120174642..120177317,2	MCF-7	breast:
2	chr11:120126928..120129765-chr11:120172517..120174089,2	MCF-7	breast:
3	chr11:119992154..119994463-chr11:120170248..120173038,2	MCF-7	breast:
4	chr11:120101055..120116563-chr11:120160593..120179156,52	K562	blood:
5	chr11:120099434..120101938-chr11:120172403..120174898,2	K562	blood:
6	chr11:120104352..120110604-chr11:120164438..120175098,43	MCF-7	breast:
7	chr11:120039493..120041713-chr11:120171400..120173344,2	MCF-7	breast:
8	chr11:120172516..120174094-chr11:120193101..120194869,2	MCF-7	breast:
9	chr11:120105406..120106378-chr11:120172236..120174440,21	K562	blood:
10	chr11:120172447..120175021-chr11:120193864..120196695,3	MCF-7	breast:
11	chr11:120104420..120112680-chr11:120168705..120181524,41	K562	blood:
12	chr11:120104320..120113596-chr11:120167938..120177639,38	MCF-7	breast:

No data

Variant related genes	Relation type
POU2F3	TF binding region
ENSG00000137699	Chromatin interaction
ENSG00000176984	Chromatin interaction
ENSG00000181264	Chromatin interaction
ENSG00000137709	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11217797	0.86[JPT][hapmap]
rs11217799	0.86[JPT][hapmap]
rs11217802	0.83[ASN][1000 genomes]
rs11217803	0.83[ASN][1000 genomes]
rs11217804	0.83[ASN][1000 genomes]
rs11217805	0.83[ASN][1000 genomes]
rs11217806	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11217807	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11217809	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11217810	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11217813	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12224052	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12225696	0.83[ASN][1000 genomes]
rs12226688	1.00[EUR][1000 genomes]
rs12576881	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2298579	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4142654	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4616049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7122401	0.80[JPT][hapmap]
rs744984	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3824883	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120169600-120178200	Enhancers	Placenta	Placenta
2	chr11:120170800-120173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:120170800-120173600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:120170800-120174600	Weak transcription	HMEC	breast
5	chr11:120170800-120174800	Weak transcription	Hela-S3	cervix
6	chr11:120170800-120175200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:120170800-120175200	Weak transcription	Small Intestine	intestine
8	chr11:120170800-120175800	Weak transcription	A549	lung
9	chr11:120170800-120176200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:120170800-120176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:120171000-120174000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:120171200-120173000	Weak transcription	NHEK	skin
13	chr11:120171200-120175400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:120172000-120173400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr11:120172000-120177600	Enhancers	Stomach Mucosa	stomach
16	chr11:120172200-120172800	Enhancers	GM12878-XiMat	blood
17	chr11:120172200-120173200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:120172200-120173800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:120172200-120173800	Enhancers	Gastric	stomach
20	chr11:120172200-120173800	Enhancers	Lung	lung
21	chr11:120172200-120174000	Enhancers	Colonic Mucosa	Colon
22	chr11:120172200-120174000	Enhancers	Duodenum Mucosa	Duodenum
23	chr11:120172200-120174200	Enhancers	Esophagus	oesophagus
24	chr11:120172200-120177600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:120172400-120172800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr11:120172400-120173200	Enhancers	Fetal Intestine Large	intestine
27	chr11:120172400-120173400	Enhancers	Liver	Liver
28	chr11:120172400-120173800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr11:120172400-120173800	Enhancers	Fetal Intestine Small	intestine
30	chr11:120172400-120173800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr11:120172400-120178200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:120172600-120172800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr11:120172600-120173800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr11:120172600-120173800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:120172600-120173800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links