Variant report

Variant	rs12325171
Chromosome Location	chr16:72118880-72118881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72041183..72043806-chr16:72118863..72121421,3	MCF-7	breast:
2	chr16:72117553..72119364-chr16:72127046..72129363,2	MCF-7	breast:
3	chr16:72107601..72110331-chr16:72118448..72121540,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140830	Chromatin interaction
ENSG00000140829	Chromatin interaction
ENSG00000261701	Chromatin interaction
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1049933	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12325593	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs13332560	0.85[AMR][1000 genomes]
rs13333207	0.85[AMR][1000 genomes]
rs13334681	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13335854	0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs13338949	1.00[AMR][1000 genomes]
rs16970697	1.00[AMR][1000 genomes]
rs16973640	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973723	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs28455724	0.85[AMR][1000 genomes]
rs28483075	0.85[AMR][1000 genomes]
rs28507713	1.00[AMR][1000 genomes]
rs28557204	1.00[AMR][1000 genomes]
rs28610193	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28639994	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35184823	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4788614	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs56978453	1.00[AMR][1000 genomes]
rs57024912	0.85[AMR][1000 genomes]
rs61074815	1.00[AMR][1000 genomes]
rs7184834	0.95[YRI][hapmap]
rs7186117	0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs7186448	1.00[AMR][1000 genomes]
rs7188150	0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs7188462	1.00[AMR][1000 genomes]
rs7189506	0.94[YRI][hapmap];0.85[AMR][1000 genomes]
rs7189654	0.82[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs7191270	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7191499	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7194569	1.00[AMR][1000 genomes]
rs7202157	0.83[AMR][1000 genomes]
rs7202158	0.83[AMR][1000 genomes]
rs7203195	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs73578560	1.00[AMR][1000 genomes]
rs73580679	1.00[AMR][1000 genomes]
rs73582412	1.00[AMR][1000 genomes]
rs8045316	0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs8047881	1.00[YRI][hapmap]
rs8051438	0.85[AMR][1000 genomes]
rs8052025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8055216	1.00[AMR][1000 genomes]
rs8056409	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8056752	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8057379	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs8061292	0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs8061439	0.85[AMR][1000 genomes]
rs9921052	0.85[AMR][1000 genomes]
rs9921752	0.82[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs9923961	1.00[AMR][1000 genomes]
rs9925476	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs9925493	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9928784	1.00[MEX][hapmap]
rs9932236	0.82[ASW][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs9932742	0.93[MKK][hapmap]
rs9933867	0.85[AMR][1000 genomes]
rs9934521	1.00[AMR][1000 genomes]
rs9940996	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs9972770	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
9	esv1808086	chr16:72088669-72128767	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a
10	esv3343168	chr16:72111500-72128436	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72106600-72126400	Weak transcription	Small Intestine	intestine
2	chr16:72108000-72126400	Weak transcription	Fetal Heart	heart
3	chr16:72108400-72119000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr16:72109000-72122600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr16:72110200-72122800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr16:72111000-72120000	Weak transcription	NHLF	lung
7	chr16:72116800-72119000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr16:72117000-72119400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr16:72117000-72126600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr16:72117200-72119600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr16:72117800-72119200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
12	chr16:72117800-72119200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:72117800-72119200	ZNF genes & repeats	Thymus	Thymus
14	chr16:72117800-72119200	ZNF genes & repeats	A549	lung
15	chr16:72117800-72119400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr16:72117800-72119400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
17	chr16:72117800-72119400	ZNF genes & repeats	Primary B cells from cord blood	blood
18	chr16:72117800-72119400	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr16:72117800-72119400	ZNF genes & repeats	Esophagus	oesophagus
20	chr16:72117800-72119400	ZNF genes & repeats	Fetal Stomach	stomach
21	chr16:72117800-72119600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr16:72117800-72119600	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr16:72117800-72124400	Strong transcription	Brain Angular Gyrus	brain
24	chr16:72117800-72124600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:72117800-72125000	Strong transcription	Brain Hippocampus Middle	brain
26	chr16:72118000-72119000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:72118000-72119000	Strong transcription	Left Ventricle	heart
28	chr16:72118000-72119200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
29	chr16:72118000-72119200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr16:72118000-72119400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr16:72118000-72119400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr16:72118000-72119400	ZNF genes & repeats	Dnd41	blood
33	chr16:72118000-72119400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr16:72118000-72119600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:72118000-72120400	Strong transcription	Psoas Muscle	Psoas
36	chr16:72118000-72120600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr16:72118000-72124400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr16:72118000-72124600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr16:72118000-72124600	Strong transcription	Brain Germinal Matrix	brain
40	chr16:72118000-72124800	Strong transcription	Adipose Nuclei	Adipose
41	chr16:72118200-72119000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
42	chr16:72118200-72119000	ZNF genes & repeats	HepG2	liver
43	chr16:72118200-72119200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr16:72118200-72119200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
45	chr16:72118200-72119200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr16:72118200-72119200	ZNF genes & repeats	Ovary	ovary
47	chr16:72118200-72119400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr16:72118200-72119400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:72118200-72119400	ZNF genes & repeats	Liver	Liver
50	chr16:72118200-72119400	ZNF genes & repeats	NHEK	skin

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