Variant report

Variant	rs11072348
Chromosome Location	chr15:72462165-72462166
allele	A/C
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	NFIC	chr15:72460733-72462249	ECC-1	luminal epithelium:	n/a	chr15:72461053-72461070
2	NFIC	chr15:72460802-72462203	ECC-1	luminal epithelium:	n/a	chr15:72461053-72461070
3	ESR1	chr15:72461625-72462214	ECC-1	luminal epithelium:	n/a	n/a
4	ESR1	chr15:72461758-72462199	ECC-1	luminal epithelium:	n/a	n/a
5	ESR1	chr15:72461559-72462274	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr15:72461485-72462332	ECC-1	luminal epithelium:	n/a	chr15:72461691-72461701
7	ESR1	chr15:72461607-72462214	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr15:72461584-72462213	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72445875..72448342-chr15:72461656..72463455,2	MCF-7	breast:
2	chr15:72459257..72462704-chr15:72465780..72468461,3	MCF-7	breast:

Variant related genes	Relation type
GRAMD2	TF binding region
ENSG00000175318	Chromatin interaction
ENSG00000260173	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10851849	1.00[EUR][1000 genomes]
rs11072352	1.00[EUR][1000 genomes]
rs12593333	1.00[EUR][1000 genomes]
rs12903688	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1457030	1.00[ASW][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1598714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1800431	1.00[EUR][1000 genomes]
rs2415131	1.00[ASW][hapmap];0.97[MKK][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2856926	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2912208	1.00[EUR][1000 genomes]
rs2912209	1.00[EUR][1000 genomes]
rs2912211	1.00[EUR][1000 genomes]
rs2912212	1.00[EUR][1000 genomes]
rs2912213	1.00[EUR][1000 genomes]
rs2912218	1.00[EUR][1000 genomes]
rs2912232	1.00[EUR][1000 genomes]
rs2925647	1.00[EUR][1000 genomes]
rs2925651	1.00[EUR][1000 genomes]
rs2929516	1.00[EUR][1000 genomes]
rs2929520	1.00[EUR][1000 genomes]
rs2929523	1.00[EUR][1000 genomes]
rs2957367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2957370	1.00[EUR][1000 genomes]
rs2957371	1.00[EUR][1000 genomes]
rs2957722	1.00[EUR][1000 genomes]
rs2957749	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs2959901	1.00[EUR][1000 genomes]
rs2959902	1.00[EUR][1000 genomes]
rs2959905	1.00[EUR][1000 genomes]
rs2959907	1.00[EUR][1000 genomes]
rs2959920	1.00[EUR][1000 genomes]
rs2959928	1.00[EUR][1000 genomes]
rs2959934	1.00[EUR][1000 genomes]
rs2959936	1.00[EUR][1000 genomes]
rs2959937	1.00[EUR][1000 genomes]
rs2959942	1.00[EUR][1000 genomes]
rs35293819	1.00[EUR][1000 genomes]
rs35514603	1.00[EUR][1000 genomes]
rs4238451	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4265763	1.00[EUR][1000 genomes]
rs4461029	1.00[EUR][1000 genomes]
rs4776585	0.83[AFR][1000 genomes]
rs4776587	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4776588	1.00[EUR][1000 genomes]
rs4777487	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4777493	0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4777502	1.00[EUR][1000 genomes]
rs56168468	1.00[EUR][1000 genomes]
rs6494987	1.00[AMR][1000 genomes]
rs6494988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6494989	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6494991	1.00[AMR][1000 genomes]
rs6494995	0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170173	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171097	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173348	1.00[EUR][1000 genomes]
rs7173532	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7177512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7179691	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180934	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8032957	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs8034892	1.00[EUR][1000 genomes]
rs8037749	1.00[EUR][1000 genomes]
rs930871	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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 target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72448800-72462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:72449200-72462200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:72454400-72471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:72458600-72463600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr15:72459600-72462600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:72459800-72462400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:72459800-72463400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:72460000-72463400	Enhancers	Fetal Intestine Large	intestine
9	chr15:72460400-72462200	Enhancers	Fetal Thymus	thymus
10	chr15:72460400-72462400	Enhancers	Primary hematopoietic stem cells	blood
11	chr15:72460600-72462200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:72460600-72462200	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:72460800-72462600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:72460800-72462600	Flanking Active TSS	Placenta	Placenta
15	chr15:72461000-72462800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr15:72461000-72463200	Enhancers	Stomach Mucosa	stomach
17	chr15:72461200-72462400	Weak transcription	Gastric	stomach
18	chr15:72461200-72463600	Enhancers	Fetal Intestine Small	intestine
19	chr15:72461200-72464400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:72461400-72462200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:72461400-72466800	Weak transcription	NHEK	skin
22	chr15:72461600-72462200	Enhancers	Colonic Mucosa	Colon
23	chr15:72461600-72462200	Enhancers	Fetal Lung	lung
24	chr15:72461800-72462200	Enhancers	HMEC	breast
25	chr15:72461800-72466400	Weak transcription	Lung	lung
26	chr15:72462000-72462200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr15:72462000-72462600	Bivalent Enhancer	HepG2	liver
28	chr15:72462000-72471400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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