Variant report

Variant	rs16976220
Chromosome Location	chr15:55538860-55538861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55537413..55539041-chr15:55609880..55612041,2	MCF-7	breast:
2	chr15:55528685..55531049-chr15:55537192..55539121,2	MCF-7	breast:
3	chr15:55538333..55540219-chr15:55542009..55544600,2	MCF-7	breast:
4	chr15:55532146..55535139-chr15:55535159..55539232,4	K562	blood:
5	chr15:55536038..55538985-chr15:55542222..55544123,2	K562	blood:
6	chr15:55526209..55528745-chr15:55538036..55540440,2	K562	blood:
7	chr15:55519854..55522805-chr15:55537341..55539230,2	MCF-7	breast:
8	chr15:55538847..55540639-chr15:55576116..55578035,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000069974	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000225973	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10518805	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12324754	0.91[EUR][1000 genomes]
rs12324775	0.91[EUR][1000 genomes]
rs12438278	0.84[EUR][1000 genomes]
rs12439213	1.00[CEU][hapmap]
rs12439264	0.80[EUR][1000 genomes]
rs12439890	1.00[CEU][hapmap]
rs12440497	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12440550	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12441258	1.00[CEU][hapmap]
rs12441307	0.80[EUR][1000 genomes]
rs12442180	0.80[EUR][1000 genomes]
rs12442887	0.82[EUR][1000 genomes]
rs12442920	0.80[EUR][1000 genomes]
rs12442937	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16976218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238178	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17238220	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819000	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17819012	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs28499877	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705006	1.00[EUR][1000 genomes]
rs557254	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170936	0.90[EUR][1000 genomes]
rs7171029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177930	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8039254	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9920531	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1049977	chr15:55502508-55555694	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
2	chr15:55490000-55562800	Weak transcription	Ovary	ovary
3	chr15:55509400-55541600	Weak transcription	Small Intestine	intestine
4	chr15:55512800-55541600	Weak transcription	Colonic Mucosa	Colon
5	chr15:55514200-55540400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:55514200-55545200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:55514400-55541200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:55514600-55542600	Weak transcription	Hela-S3	cervix
9	chr15:55514600-55543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:55514800-55539800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:55514800-55560400	Weak transcription	Spleen	Spleen
12	chr15:55516000-55559600	Weak transcription	Fetal Stomach	stomach
13	chr15:55517600-55542800	Weak transcription	Thymus	Thymus
14	chr15:55517800-55539600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:55517800-55542200	Weak transcription	Fetal Thymus	thymus
16	chr15:55517800-55542800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:55518000-55539200	Weak transcription	Fetal Lung	lung
18	chr15:55518600-55539400	Weak transcription	Placenta	Placenta
19	chr15:55518800-55541200	Weak transcription	Aorta	Aorta
20	chr15:55520800-55574800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:55521000-55541400	Weak transcription	Fetal Intestine Large	intestine
22	chr15:55522800-55540600	Weak transcription	Liver	Liver
23	chr15:55522800-55543200	Weak transcription	Pancreas	Pancrea
24	chr15:55522800-55547000	Weak transcription	GM12878-XiMat	blood
25	chr15:55523200-55542600	Weak transcription	HMEC	breast
26	chr15:55526800-55543200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:55527000-55542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:55527000-55544200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:55527200-55542800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:55532800-55539200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:55532800-55539200	Weak transcription	Gastric	stomach
32	chr15:55532800-55539400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr15:55532800-55539400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:55533000-55539800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:55533200-55539000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:55533400-55539000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:55533400-55539400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:55533600-55539400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:55533800-55539600	Weak transcription	Primary T cells from cord blood	blood
40	chr15:55533800-55543400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:55534400-55539800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr15:55534400-55541600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:55534400-55545600	Weak transcription	Osteobl	bone
44	chr15:55534600-55542200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:55535000-55542200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:55535400-55539000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:55535800-55540400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:55537200-55543200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr15:55537600-55539200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr15:55537600-55539800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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