Variant report

Variant	rs1669872
Chromosome Location	chr15:52684004-52684005
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52676956..52678562-chr15:52682249..52684331,2	MCF-7	breast:
2	chr15:52683428..52686900-chr15:52692010..52696057,4	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10518683	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.96[ASN][1000 genomes]
rs1104800	1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108808	0.96[ASN][1000 genomes]
rs12101973	1.00[ASN][1000 genomes]
rs12913979	1.00[ASN][1000 genomes]
rs13329278	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs13329402	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13329500	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[ASN][1000 genomes]
rs1669870	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1669874	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16964903	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16964910	0.96[ASN][1000 genomes]
rs16964915	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16964919	0.96[ASN][1000 genomes]
rs16964921	0.96[ASN][1000 genomes]
rs16964928	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[ASN][1000 genomes]
rs16964944	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16964952	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1724577	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1724599	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1724600	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1724602	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2222656	0.85[GIH][hapmap]
rs2242059	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2414137	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2414138	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2414145	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs2414147	1.00[TSI][hapmap]
rs2600903	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2600904	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs28367336	0.96[ASN][1000 genomes]
rs28374631	0.96[ASN][1000 genomes]
rs28409636	1.00[ASN][1000 genomes]
rs28409760	1.00[ASN][1000 genomes]
rs28475475	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs28496242	0.96[ASN][1000 genomes]
rs28503750	1.00[ASN][1000 genomes]
rs28508266	0.96[ASN][1000 genomes]
rs28532168	1.00[ASN][1000 genomes]
rs28556657	1.00[ASN][1000 genomes]
rs28633243	0.96[ASN][1000 genomes]
rs28653534	0.96[ASN][1000 genomes]
rs28693941	0.96[ASN][1000 genomes]
rs28756182	1.00[ASN][1000 genomes]
rs3764230	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4624108	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4774620	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs4774621	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs7163242	1.00[ASN][1000 genomes]
rs7163778	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs7164164	0.92[ASN][1000 genomes]
rs7164872	1.00[ASN][1000 genomes]
rs7166034	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7167437	0.88[ASN][1000 genomes]
rs7168251	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7169346	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7171999	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408415	1.00[ASN][1000 genomes]
rs73408465	1.00[ASN][1000 genomes]
rs73408469	0.96[ASN][1000 genomes]
rs73408478	0.96[ASN][1000 genomes]
rs73410713	1.00[ASN][1000 genomes]
rs7342673	0.85[GIH][hapmap]
rs744501	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs8024412	1.00[GIH][hapmap]
rs8027777	0.96[ASN][1000 genomes]
rs8030307	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8035199	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs8040369	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8040558	1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs8041819	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs876549	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs9744852	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs9920739	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
3	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:52649000-52687200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:52658400-52687200	Weak transcription	Small Intestine	intestine
6	chr15:52662600-52685000	Weak transcription	Psoas Muscle	Psoas
7	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
10	chr15:52667000-52684800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:52667000-52686000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:52667000-52686600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:52667600-52684400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
15	chr15:52669400-52693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:52673800-52684800	Weak transcription	Hela-S3	cervix
17	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
19	chr15:52675000-52686200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:52676000-52684600	Weak transcription	Osteobl	bone
22	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
23	chr15:52676200-52686400	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:52676400-52684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:52676400-52685600	Weak transcription	Liver	Liver
28	chr15:52676400-52696800	Weak transcription	Brain Germinal Matrix	brain
29	chr15:52676400-52696800	Weak transcription	Dnd41	blood
30	chr15:52676400-52697000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:52676400-52701000	Weak transcription	HMEC	breast
33	chr15:52676400-52709800	Weak transcription	NHLF	lung
34	chr15:52676400-52721400	Weak transcription	Gastric	stomach
35	chr15:52676600-52689000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:52676600-52698000	Weak transcription	Fetal Thymus	thymus
37	chr15:52676600-52701800	Weak transcription	Right Ventricle	heart
38	chr15:52676600-52706400	Weak transcription	Lung	lung
39	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:52676800-52684600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:52677800-52689200	Weak transcription	Brain Anterior Caudate	brain
43	chr15:52678000-52684600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:52678400-52684600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:52679800-52684600	Weak transcription	NHEK	skin
46	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
48	chr15:52680600-52686200	Weak transcription	GM12878-XiMat	blood
49	chr15:52680600-52719800	Weak transcription	NH-A	brain
50	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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