Variant report

Variant	rs547221
Chromosome Location	chr11:65147294-65147295
allele	A/G
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	EP300	chr11:65147211-65147827	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr11:65147201-65147940	MCF-7	breast:	n/a	n/a
3	GATA3	chr11:65147252-65147889	MCF-7	breast:	n/a	n/a
4	NR2F2	chr11:65147206-65147918	MCF-7	breast:	n/a	n/a
5	ESR1	chr11:65147292-65147805	ECC-1	luminal epithelium:	n/a	chr11:65147538-65147555
6	ESR1	chr11:65147275-65147766	ECC-1	luminal epithelium:	n/a	chr11:65147538-65147555
7	ESR1	chr11:65147253-65147815	T-47D	breast:	n/a	chr11:65147538-65147555
8	ESR1	chr11:65147284-65147773	T-47D	breast:	n/a	chr11:65147538-65147555
9	GATA3	chr11:65147031-65147746	MCF-7	breast:	n/a	n/a
10	MAX	chr11:65147264-65147959	MCF-7	breast:	n/a	chr11:65147806-65147816
11	GATA3	chr11:65147275-65147802	MCF-7	breast:	n/a	n/a
12	HDAC2	chr11:65147291-65147875	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65145713..65148511-chr11:65656640..65659365,2	MCF-7	breast:
2	chr11:65147131..65148138-chr11:65185981..65186782,7	MCF-7	breast:
3	chr11:65116402..65157784-chr11:65261420..65278410,154	K562	blood:
4	chr11:65098911..65102850-chr11:65147012..65151675,4	MCF-7	breast:
5	chr11:65147249..65148062-chr11:65185872..65186473,2	MCF-7	breast:
6	chr11:65145756..65147561-chr11:65226318..65228279,2	K562	blood:

Variant related genes	Relation type
SLC25A45	TF binding region
ENSG00000251562	Chromatin interaction
ENSG00000133884	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000270117	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2073799	0.86[EUR][1000 genomes]
rs2073800	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930154	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs578270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585210	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs651283	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs652501	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs666194	0.89[GIH][hapmap]
rs681309	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs547221	TPCN2	cis	parietal	SCAN
rs547221	CDK2AP2	cis	cerebellum	SCAN
rs547221	NEAT1	cis	Muscle Skeletal	GTEx
rs547221	HRASLS2	cis	parietal	SCAN
rs547221	SLC22A24	cis	parietal	SCAN
rs547221	SDHAF2	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65134200-65149200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:65134400-65149400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:65135600-65147400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:65138800-65147600	Weak transcription	Right Ventricle	heart
5	chr11:65138800-65149400	Weak transcription	Aorta	Aorta
6	chr11:65139200-65148200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:65139400-65147800	Weak transcription	Psoas Muscle	Psoas
8	chr11:65139400-65148400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:65140000-65148400	Weak transcription	K562	blood
10	chr11:65140000-65149200	Weak transcription	HSMM	muscle
11	chr11:65140400-65149200	Weak transcription	Right Atrium	heart
12	chr11:65141000-65149200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:65141600-65148400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:65142000-65147400	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:65142000-65148200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:65142000-65148200	Weak transcription	Left Ventricle	heart
17	chr11:65142200-65148200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:65142600-65148000	Strong transcription	Primary T cells from cord blood	blood
19	chr11:65143000-65147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:65143000-65148200	Weak transcription	HMEC	breast
21	chr11:65143000-65148400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:65143200-65147400	Weak transcription	Esophagus	oesophagus
23	chr11:65143200-65147400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:65143200-65148200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:65144000-65148000	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr11:65144200-65148200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr11:65144200-65148200	Strong transcription	Thymus	Thymus
28	chr11:65144200-65149200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:65144600-65147600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr11:65144800-65149200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr11:65145200-65148400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:65145400-65147600	Weak transcription	Fetal Heart	heart
33	chr11:65145400-65148200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:65145600-65149200	Weak transcription	Fetal Stomach	stomach
35	chr11:65145800-65147600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:65145800-65147600	Weak transcription	Stomach Mucosa	stomach
37	chr11:65145800-65148400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:65145800-65148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:65145800-65148600	Enhancers	A549	lung
40	chr11:65145800-65149200	Weak transcription	Brain Substantia Nigra	brain
41	chr11:65146000-65148400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:65146200-65147600	Transcr. at gene 5' and 3'	Pancreas	Pancrea
43	chr11:65146200-65147800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:65146200-65148000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:65146200-65148400	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr11:65146200-65150800	Enhancers	Gastric	stomach
47	chr11:65146400-65147400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:65146400-65147600	Weak transcription	Colonic Mucosa	Colon
49	chr11:65146400-65148200	Weak transcription	Placenta	Placenta
50	chr11:65146400-65148400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links