Variant report

Variant	rs1542374
Chromosome Location	chr15:33419334-33419335
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	chr15:33359725..33362566-chr15:33418039..33421001,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1542375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1971219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444959	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2444963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468734	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345760	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs921783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33411800-33420200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:33416600-33420400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:33417200-33419600	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr15:33417400-33420200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr15:33417800-33419400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr15:33417800-33419600	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:33418000-33419400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:33418000-33419600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:33418000-33420200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr15:33418200-33419400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr15:33418200-33419400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:33418200-33419400	Enhancers	Spleen	Spleen
13	chr15:33418200-33419600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr15:33418200-33419800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:33418200-33419800	Enhancers	HMEC	breast
16	chr15:33418200-33420000	Enhancers	Fetal Muscle Leg	muscle
17	chr15:33418200-33420200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:33418200-33420600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:33418400-33419400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr15:33418400-33419400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr15:33418400-33419400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:33418400-33419400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:33418400-33419400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr15:33418400-33419400	Enhancers	Fetal Intestine Small	intestine
25	chr15:33418400-33419400	Enhancers	Stomach Mucosa	stomach
26	chr15:33418400-33419600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr15:33418400-33419600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:33418400-33419600	Enhancers	Fetal Intestine Large	intestine
29	chr15:33418400-33419600	Flanking Active TSS	Fetal Kidney	kidney
30	chr15:33418400-33419600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr15:33418400-33419600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:33418400-33419600	Enhancers	NH-A	brain
33	chr15:33418400-33419600	Enhancers	NHEK	skin
34	chr15:33418600-33419400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:33418600-33419400	Enhancers	Fetal Heart	heart
36	chr15:33418600-33419400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr15:33418600-33419800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr15:33418600-33420200	Enhancers	Hela-S3	cervix
39	chr15:33418800-33419400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:33418800-33419400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:33418800-33419400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:33418800-33419400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr15:33418800-33419400	Flanking Active TSS	Osteobl	bone
44	chr15:33418800-33419600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr15:33418800-33419600	Flanking Active TSS	NHLF	lung
46	chr15:33418800-33421000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:33419000-33419400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:33419000-33419400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:33419000-33419400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr15:33419000-33419400	Flanking Active TSS	HSMM	muscle

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