Variant report

Variant	rs2600904
Chromosome Location	chr15:52679747-52679748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52650282..52651929-chr15:52678734..52680438,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10518683	1.00[GIH][hapmap]
rs10518688	1.00[ASN][1000 genomes]
rs12913979	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13329278	1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs13329417	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13329500	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap]
rs1669870	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1669872	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16964891	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16964903	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs16964910	1.00[JPT][hapmap]
rs16964924	0.93[ASN][1000 genomes]
rs16964927	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16964928	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap]
rs16964935	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16964944	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs16964952	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1724577	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2414145	1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2600903	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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693458	0.80[AFR][1000 genomes]
rs28366864	1.00[ASN][1000 genomes]
rs28367508	0.93[ASN][1000 genomes]
rs28415069	0.93[ASN][1000 genomes]
rs28415349	0.93[ASN][1000 genomes]
rs28415472	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28421476	0.87[ASN][1000 genomes]
rs28426997	1.00[ASN][1000 genomes]
rs28444393	1.00[ASN][1000 genomes]
rs28462026	1.00[ASN][1000 genomes]
rs28475475	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs28479614	0.93[ASN][1000 genomes]
rs28480975	0.93[ASN][1000 genomes]
rs28485251	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28488423	1.00[ASN][1000 genomes]
rs28499517	0.87[ASN][1000 genomes]
rs28514341	0.93[ASN][1000 genomes]
rs28515624	0.93[ASN][1000 genomes]
rs28534436	1.00[ASN][1000 genomes]
rs28538563	1.00[ASN][1000 genomes]
rs28564655	0.93[ASN][1000 genomes]
rs28590330	1.00[ASN][1000 genomes]
rs28594692	0.93[ASN][1000 genomes]
rs28605633	0.93[ASN][1000 genomes]
rs28613360	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28618215	1.00[ASN][1000 genomes]
rs28638475	1.00[ASN][1000 genomes]
rs28649737	0.93[ASN][1000 genomes]
rs28650960	0.93[ASN][1000 genomes]
rs28655190	1.00[ASN][1000 genomes]
rs28660682	0.93[ASN][1000 genomes]
rs28661501	0.93[ASN][1000 genomes]
rs28663524	0.87[ASN][1000 genomes]
rs28669685	1.00[ASN][1000 genomes]
rs28682547	0.87[ASN][1000 genomes]
rs28697879	0.93[ASN][1000 genomes]
rs28729511	0.87[ASN][1000 genomes]
rs28735959	1.00[ASN][1000 genomes]
rs4499185	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4774620	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4774621	1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4776042	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987194	1.00[ASN][1000 genomes]
rs57864537	0.93[ASN][1000 genomes]
rs58029714	0.93[ASN][1000 genomes]
rs58812575	1.00[ASN][1000 genomes]
rs7163569	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163778	1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164722	1.00[ASN][1000 genomes]
rs7166034	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7167181	0.93[ASN][1000 genomes]
rs7167680	0.93[ASN][1000 genomes]
rs7167890	0.88[ASN][1000 genomes]
rs7167916	1.00[ASN][1000 genomes]
rs7168076	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7169104	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7169346	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs7170622	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7178069	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7179156	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7182148	0.88[ASN][1000 genomes]
rs73408408	0.93[ASN][1000 genomes]
rs73410715	1.00[ASN][1000 genomes]
rs73410759	1.00[ASN][1000 genomes]
rs7342673	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs744501	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs8023623	1.00[ASN][1000 genomes]
rs8024412	1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8024624	0.93[ASN][1000 genomes]
rs8027637	0.93[ASN][1000 genomes]
rs8030307	0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035199	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs8041819	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs8042235	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8042245	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs876549	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9744852	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9920195	0.87[ASN][1000 genomes]
rs9920749	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	chr15:52644200-52680800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
4	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:52649000-52687200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52658400-52687200	Weak transcription	Small Intestine	intestine
7	chr15:52662600-52683600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:52662600-52685000	Weak transcription	Psoas Muscle	Psoas
9	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
12	chr15:52667000-52682000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:52667000-52684800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:52667000-52686000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:52667000-52686600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:52667600-52684400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:52668000-52683400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:52668800-52683800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
20	chr15:52669200-52683400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:52669400-52693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:52671200-52682000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:52671400-52681400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:52672400-52684000	Weak transcription	Fetal Heart	heart
25	chr15:52673800-52683800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:52673800-52684800	Weak transcription	Hela-S3	cervix
27	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
29	chr15:52674800-52681400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr15:52675000-52686200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:52676000-52683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:52676000-52684600	Weak transcription	Osteobl	bone
34	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
35	chr15:52676200-52679800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:52676200-52683400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:52676200-52686400	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:52676400-52680000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:52676400-52680400	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:52676400-52683000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:52676400-52683200	Weak transcription	A549	lung
44	chr15:52676400-52683600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:52676400-52684000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr15:52676400-52684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:52676400-52685600	Weak transcription	Liver	Liver
48	chr15:52676400-52696800	Weak transcription	Brain Germinal Matrix	brain
49	chr15:52676400-52696800	Weak transcription	Dnd41	blood
50	chr15:52676400-52697000	Weak transcription	Rectal Smooth Muscle	rectum

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