Variant report

Variant	rs6493570
Chromosome Location	chr15:52960264-52960265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52946056..52948651-chr15:52958978..52960779,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10775148	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10775149	0.87[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070904	1.00[CEU][hapmap]
rs11070910	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11629479	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634879	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102061	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12900462	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12908944	0.85[EUR][1000 genomes]
rs12916276	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12916405	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2414162	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2414165	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2414168	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414169	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414170	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414171	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414174	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414176	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414177	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28402931	0.83[AFR][1000 genomes]
rs2899493	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34340005	0.85[EUR][1000 genomes]
rs35756938	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35760898	0.90[EUR][1000 genomes]
rs4386077	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4404000	1.00[CEU][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774635	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776064	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62025584	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62025586	1.00[EUR][1000 genomes]
rs7162184	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166478	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7168045	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7169849	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7179310	1.00[CEU][hapmap]
rs8026304	0.83[AMR][1000 genomes]
rs8026469	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8032889	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8035115	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8036671	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8036680	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8040787	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042646	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs933858	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs933859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9806267	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:52944600-52962000	Weak transcription	Aorta	Aorta
6	chr15:52944600-52965000	Strong transcription	Primary B cells from cord blood	blood
7	chr15:52944600-52965400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
9	chr15:52945000-52965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:52945000-52968600	Weak transcription	HepG2	liver
11	chr15:52945400-52965400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:52945600-52962800	Strong transcription	Placenta	Placenta
13	chr15:52946000-52962000	Weak transcription	Right Ventricle	heart
14	chr15:52946000-52962000	Weak transcription	Spleen	Spleen
15	chr15:52946000-52965200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:52946000-52968200	Weak transcription	Fetal Heart	heart
17	chr15:52946000-52968600	Weak transcription	Stomach Mucosa	stomach
18	chr15:52949200-52965400	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr15:52949200-52965600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:52949400-52966400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr15:52950000-52962000	Weak transcription	NHLF	lung
22	chr15:52950400-52965800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:52950400-52965800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:52950400-52969400	Weak transcription	A549	lung
25	chr15:52950800-52960600	Strong transcription	Fetal Lung	lung
26	chr15:52950800-52968400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:52951000-52965600	Strong transcription	Adipose Nuclei	Adipose
28	chr15:52951000-52970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:52951200-52960800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:52952000-52967400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr15:52952000-52968000	Strong transcription	Fetal Thymus	thymus
32	chr15:52952200-52967800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:52952400-52960600	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:52952400-52960600	Strong transcription	HSMMtube	muscle
35	chr15:52952400-52963600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:52952400-52966200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:52952600-52960800	Strong transcription	Primary T cells from cord blood	blood
38	chr15:52952800-52960400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:52953000-52963200	Weak transcription	Psoas Muscle	Psoas
40	chr15:52953200-52965800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr15:52953200-52967800	Weak transcription	Fetal Intestine Small	intestine
42	chr15:52953600-52965000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:52953800-52963000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:52954800-52962000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:52955200-52960600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr15:52955200-52962000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:52955600-52963000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:52955800-52960400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:52956000-52960800	Strong transcription	Brain Anterior Caudate	brain
50	chr15:52956200-52960400	Strong transcription	Brain Inferior Temporal Lobe	brain

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