Variant report

Variant	rs12440929
Chromosome Location	chr15:52680276-52680277
allele	C/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: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12438578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441597	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12442531	0.84[AMR][1000 genomes]
rs12900962	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12901814	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1405183	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1405184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1581580	0.84[AMR][1000 genomes]
rs17707852	0.92[YRI][hapmap]
rs1965563	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2290332	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2290335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2290336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28533733	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3794557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3794564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3794565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7176600	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7176830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030535	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8032995	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8041275	0.83[AMR][1000 genomes]
rs871488	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs940970	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[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	chr15:52676200-52683400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:52676200-52686400	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:52676400-52680400	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:52676400-52683000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr15:52676400-52683200	Weak transcription	A549	lung
42	chr15:52676400-52683600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:52676400-52684000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:52676400-52684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr15:52676400-52685600	Weak transcription	Liver	Liver
46	chr15:52676400-52696800	Weak transcription	Brain Germinal Matrix	brain
47	chr15:52676400-52696800	Weak transcription	Dnd41	blood
48	chr15:52676400-52697000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:52676400-52701000	Weak transcription	HMEC	breast

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