Variant report

Variant	rs12438578
Chromosome Location	chr15:52649440-52649441
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:121483254..121484811-chr15:52648576..52650665,2	MCF-7	breast:
2	chr15:52648218..52650627-chr15:52655549..52658178,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12440929	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	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900962	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12901814	0.81[AMR][1000 genomes]
rs1405183	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1405184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17707852	0.85[JPT][hapmap];0.92[YRI][hapmap]
rs1965563	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2290332	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2414139	0.80[YRI][hapmap]
rs2462847	0.80[JPT][hapmap]
rs28533733	0.83[AMR][1000 genomes]
rs3794557	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs3794564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176600	0.83[AMR][1000 genomes]
rs7176830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8025937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8030535	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs871488	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs940970	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
2	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:52611800-52675800	Weak transcription	Gastric	stomach
5	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
6	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
7	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
9	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
10	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
11	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
13	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:52632800-52657400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:52632800-52662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:52633600-52662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:52640200-52655000	Weak transcription	Liver	Liver
19	chr15:52640600-52666600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:52641800-52666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:52643600-52655600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:52643800-52650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:52643800-52654000	Weak transcription	Osteobl	bone
24	chr15:52643800-52655400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:52644000-52650200	Weak transcription	Ovary	ovary
26	chr15:52644000-52664200	Weak transcription	NHLF	lung
27	chr15:52644000-52666600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:52644200-52661000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:52644200-52680800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:52644600-52650000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:52644600-52650000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:52644600-52650000	Weak transcription	NHDF-Ad	bronchial
33	chr15:52644600-52650200	Weak transcription	Pancreas	Pancrea
34	chr15:52644600-52650400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:52644600-52652000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:52644600-52652200	Weak transcription	Aorta	Aorta
37	chr15:52644600-52653400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr15:52644600-52654200	Weak transcription	Right Atrium	heart
39	chr15:52644600-52660200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:52644600-52661200	Weak transcription	Thymus	Thymus
41	chr15:52644600-52661600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:52644600-52662000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr15:52644600-52662200	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:52644600-52662400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:52644600-52662400	Weak transcription	Fetal Stomach	stomach
46	chr15:52644600-52663800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:52644600-52663800	Weak transcription	Spleen	Spleen
48	chr15:52644600-52665400	Weak transcription	A549	lung
49	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
50	chr15:52644800-52650200	Weak transcription	Muscle Satellite Cultured Cells	--

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