Variant report

Variant	rs28544576
Chromosome Location	chr8:10996985-10996986
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	RAD21	chr8:10996540-10997401	SK-N-SH	brain:	n/a	chr8:10996867-10996880 chr8:10996986-10997000 chr8:10996899-10996906
2	RAD21	chr8:10996730-10997116	H1-hESC	embryonic stem cell:	n/a	chr8:10996867-10996880 chr8:10996986-10997000 chr8:10996899-10996906
3	REST	chr8:10996759-10997142	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr8:10996788-10997008	H1-hESC	embryonic stem cell:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
5	CTCF	chr8:10996645-10997299	SK-N-SH	brain:	n/a	chr8:10996901-10996909 chr8:10997049-10997057 chr8:10996892-10996905
6	CTCF	chr8:10996715-10997099	H1-hESC	embryonic stem cell:	n/a	chr8:10996901-10996909 chr8:10997049-10997057 chr8:10996892-10996905
7	MXI1	chr8:10996474-10997773	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr8:10996971-10996988	MCF-7	breast:	n/a	n/a
9	CTCF	chr8:10996716-10996997	H1-hESC	embryonic stem cell:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
10	CTCF	chr8:10996860-10997010	HCPEpiC	choroid plexus:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
11	RAD21	chr8:10996768-10997162	H1-hESC	embryonic stem cell:	n/a	chr8:10996867-10996880 chr8:10996986-10997000 chr8:10996899-10996906
12	EP300	chr8:10996803-10997109	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr8:10996860-10997010	GM12869	blood:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
14	RAD21	chr8:10996741-10997066	SK-N-SH_RA	brain:	n/a	chr8:10996867-10996880 chr8:10996986-10997000 chr8:10996899-10996906
15	CTCF	chr8:10996860-10997010	SK-N-SH_RA	brain:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
16	CTCF	chr8:10996860-10997010	GM12872	blood:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
17	ZNF143	chr8:10996811-10997107	H1-hESC	embryonic stem cell:	n/a	chr8:10996868-10996887
18	CTCF	chr8:10996900-10997050	GM12868	blood:	n/a	chr8:10996901-10996909
19	RAD21	chr8:10996737-10997175	H1-hESC	embryonic stem cell:	n/a	chr8:10996867-10996880 chr8:10996986-10997000 chr8:10996899-10996906
20	SMC3	chr8:10996574-10997375	SK-N-SH	brain:	n/a	n/a
21	RAD21	chr8:10996772-10997082	SK-N-SH_RA	brain:	n/a	chr8:10996867-10996880 chr8:10996986-10997000 chr8:10996899-10996906
22	EP300	chr8:10996436-10997507	SK-N-SH	brain:	n/a	chr8:10997482-10997491
23	CTCF	chr8:10996880-10997030	RPTEC	kidney:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
24	CTCF	chr8:10996860-10997010	HEK293	kidney:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
25	CTCF	chr8:10996840-10996990	GM12871	blood:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
26	CTCF	chr8:10996860-10997010	BE2_C	brain:	n/a	chr8:10996901-10996909 chr8:10996892-10996905
27	TBP	chr8:10996773-10997071	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10987323..10988888-chr8:10996311..10998461,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254556	TF binding region
ENSG00000215346	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10282848	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17152881	0.87[ASN][1000 genomes]
rs17152921	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17152930	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17152938	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17725809	0.87[ASN][1000 genomes]
rs4270924	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7003183	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73547435	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812339	0.87[ASN][1000 genomes]
rs7844248	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9329237	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025426	chr8:10942929-11037903	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1026331	chr8:10955941-11046394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1019796	chr8:10979442-11010826	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10966200-10999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:10982800-11003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr8:10983000-11002000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:10983000-11003200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr8:10983200-10997000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr8:10983200-11001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:10984400-11000000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:10986400-11002000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:10987200-10997000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr8:10989600-11014200	Weak transcription	Pancreas	Pancrea
12	chr8:10991800-10998800	Weak transcription	Gastric	stomach
13	chr8:10991800-11011800	Weak transcription	Left Ventricle	heart
14	chr8:10992800-11002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:10994400-10997000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:10994800-10997000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr8:10995600-10997000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr8:10995600-10999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr8:10996800-10997000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:10996800-10997000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:10996800-10997200	Enhancers	Esophagus	oesophagus
22	chr8:10996800-10997200	Enhancers	Fetal Muscle Trunk	muscle
23	chr8:10996800-10997400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr8:10996800-10997400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:10996800-10997400	Enhancers	Spleen	Spleen
26	chr8:10996800-10997600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr8:10996800-10998000	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links