Variant report

Variant	rs28417106
Chromosome Location	chr15:55574616-55574617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55527813..55534361-chr15:55567580..55576356,11	K562	blood:
2	chr15:55514268..55516537-chr15:55573502..55575651,2	K562	blood:
3	chr15:55572666..55574858-chr15:55699937..55702712,2	K562	blood:
4	chr15:55574462..55576486-chr15:55577587..55580310,2	MCF-7	breast:
5	chr15:55510011..55511659-chr15:55574355..55576916,2	MCF-7	breast:
6	chr15:55520021..55524159-chr15:55571941..55574919,3	K562	blood:
7	chr15:55572408..55575581-chr15:55726220..55729674,3	K562	blood:

Variant related genes	Relation type
ENSG00000261652	Chromatin interaction
ENSG00000260916	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs16976260	0.81[AFR][1000 genomes]
rs28407079	1.00[AMR][1000 genomes]
rs28445247	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28544417	0.89[AFR][1000 genomes]
rs28659952	0.81[AFR][1000 genomes]
rs55741428	0.84[AFR][1000 genomes]
rs55904532	1.00[AMR][1000 genomes]
rs56815391	0.88[AFR][1000 genomes]
rs56849426	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58851760	1.00[AMR][1000 genomes]
rs59652532	1.00[AMR][1000 genomes]
rs59887243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60146363	1.00[AMR][1000 genomes]
rs61019518	1.00[AMR][1000 genomes]
rs61044972	0.85[AMR][1000 genomes]
rs61176773	0.88[AFR][1000 genomes]
rs7165133	0.89[AFR][1000 genomes]
rs7177224	1.00[AMR][1000 genomes]
rs73406933	1.00[AMR][1000 genomes]
rs73406996	1.00[AMR][1000 genomes]
rs73408819	1.00[AMR][1000 genomes]
rs73408848	1.00[AMR][1000 genomes]
rs73408869	1.00[AMR][1000 genomes]
rs73413697	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73415503	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74015565	0.86[AFR][1000 genomes]
rs74015569	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569522	chr15:55532211-55611126	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904241	chr15:55534342-55611126	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv904242	chr15:55550755-55611126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv569524	chr15:55558624-55612511	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55520800-55574800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:55542400-55581000	Weak transcription	Fetal Intestine Small	intestine
3	chr15:55548600-55574800	Weak transcription	Left Ventricle	heart
4	chr15:55553200-55581000	Weak transcription	Fetal Intestine Large	intestine
5	chr15:55560200-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:55560200-55575400	Weak transcription	Thymus	Thymus
7	chr15:55561600-55576600	Weak transcription	Liver	Liver
8	chr15:55563800-55574800	Weak transcription	Lung	lung
9	chr15:55565000-55574800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr15:55567800-55580800	Weak transcription	Fetal Stomach	stomach
11	chr15:55568400-55574800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:55569400-55578200	Weak transcription	Fetal Kidney	kidney
13	chr15:55570200-55580400	Weak transcription	Fetal Thymus	thymus
14	chr15:55570200-55581200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:55570600-55580800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:55571200-55575600	Weak transcription	Fetal Lung	lung
17	chr15:55571200-55577800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr15:55571800-55575200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:55572000-55580800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:55572200-55581000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:55572400-55574800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:55572400-55580800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:55572600-55574800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:55572600-55574800	Weak transcription	Pancreas	Pancrea
25	chr15:55572600-55574800	Weak transcription	Spleen	Spleen
26	chr15:55572600-55575800	Enhancers	Hela-S3	cervix
27	chr15:55572600-55580000	Weak transcription	HepG2	liver
28	chr15:55572600-55581000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:55573200-55578200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr15:55573200-55579000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr15:55573400-55575600	Enhancers	GM12878-XiMat	blood
32	chr15:55573400-55577400	Genic enhancers	K562	blood
33	chr15:55573600-55574800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr15:55573600-55574800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:55573600-55579600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr15:55573800-55574800	Enhancers	Primary B cells from cord blood	blood
37	chr15:55573800-55575200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:55573800-55575200	Enhancers	Gastric	stomach
39	chr15:55573800-55575400	Enhancers	NHDF-Ad	bronchial
40	chr15:55573800-55575400	Enhancers	NHLF	lung
41	chr15:55573800-55575800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:55573800-55575800	Enhancers	HUVEC	blood vessel
43	chr15:55573800-55576200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr15:55573800-55576200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr15:55573800-55577000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:55573800-55578400	Enhancers	Primary hematopoietic stem cells	blood
47	chr15:55574000-55575200	Enhancers	NHEK	skin
48	chr15:55574000-55575600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:55574000-55575600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:55574000-55575800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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