Variant report

Variant	rs12440497
Chromosome Location	chr15:55510211-55510212
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55506823..55512825-chr15:55581621..55584797,8	K562	blood:
2	chr15:55508852..55510864-chr15:55611127..55612962,2	MCF-7	breast:
3	chr15:55504623..55507168-chr15:55508677..55511690,3	K562	blood:
4	chr15:55509415..55510514-chr15:55582030..55583628,14	K562	blood:
5	chr15:55508435..55511802-chr15:55609851..55613340,4	K562	blood:
6	chr15:55509907..55510441-chr15:55581136..55581807,2	MCF-7	breast:
7	chr15:55506823..55513814-chr15:55580257..55584341,9	K562	blood:
8	chr15:55502637..55507829-chr15:55507957..55511534,4	MCF-7	breast:
9	chr15:55510011..55511659-chr15:55574355..55576916,2	MCF-7	breast:
10	chr15:55510048..55513584-chr15:55529255..55531820,4	K562	blood:
11	chr15:55507731..55513408-chr15:55580265..55584053,9	MCF-7	breast:
12	chr15:55509736..55510399-chr15:55727358..55727891,2	MCF-7	breast:
13	chr15:55485223..55489171-chr15:55508275..55513421,7	K562	blood:
14	chr15:55509498..55510422-chr15:55731553..55732482,2	K562	blood:
15	chr15:55509687..55510456-chr15:55700271..55700912,2	MCF-7	breast:
16	chr15:55508422..55515195-chr15:55580692..55586566,10	MCF-7	breast:
17	chr15:55505618..55507168-chr15:55508897..55511690,2	K562	blood:
18	chr15:55509049..55510463-chr15:55582084..55583305,19	MCF-7	breast:
19	chr15:55509574..55510417-chr15:55731604..55732340,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261652	Chromatin interaction
ENSG00000225973	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000137876	Chromatin interaction
ENSG00000069943	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10518803	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10518805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324754	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324775	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438278	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439890	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12440550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441307	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442180	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442887	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442920	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976218	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16976220	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16976227	1.00[CEU][hapmap]
rs16976229	1.00[CEU][hapmap]
rs16976231	1.00[CEU][hapmap]
rs17238178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238192	0.82[AMR][1000 genomes]
rs17238199	0.82[AMR][1000 genomes]
rs17238206	0.82[AMR][1000 genomes]
rs17238220	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17819000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819024	0.82[AMR][1000 genomes]
rs17819036	0.83[AMR][1000 genomes]
rs28499877	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28705006	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557254	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61638549	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7170936	1.00[ASN][1000 genomes]
rs7171029	1.00[CEU][hapmap]
rs7171897	1.00[CEU][hapmap]
rs7173803	1.00[ASN][1000 genomes]
rs7177930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489600-55513200	Weak transcription	Lung	lung
2	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
3	chr15:55490000-55513000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:55490000-55513200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:55490000-55513200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:55490000-55513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:55490000-55517200	Weak transcription	Aorta	Aorta
8	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:55490000-55562800	Weak transcription	Ovary	ovary
10	chr15:55490200-55511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:55490200-55511400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:55490200-55511400	Weak transcription	Osteobl	bone
13	chr15:55490200-55513200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:55490200-55513800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:55490200-55514000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:55490400-55512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:55491000-55513600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:55497800-55511200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:55497800-55513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:55497800-55513000	Weak transcription	Hela-S3	cervix
21	chr15:55497800-55514000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:55497800-55518400	Weak transcription	Gastric	stomach
23	chr15:55498000-55510400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:55498000-55512800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:55498000-55512800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:55498000-55513200	Weak transcription	Primary T cells from cord blood	blood
27	chr15:55498000-55513400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:55498000-55514200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:55498400-55512400	Weak transcription	Fetal Stomach	stomach
30	chr15:55506000-55514000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:55507000-55513000	Weak transcription	Fetal Intestine Small	intestine
32	chr15:55507400-55511200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:55508400-55517000	Weak transcription	Fetal Heart	heart
34	chr15:55508600-55513200	Weak transcription	Thymus	Thymus
35	chr15:55508600-55522600	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:55509000-55511200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:55509000-55512600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr15:55509000-55513000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:55509400-55511200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr15:55509400-55541600	Weak transcription	Small Intestine	intestine
41	chr15:55509600-55510400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr15:55509600-55510600	Enhancers	Primary B cells from peripheral blood	blood
43	chr15:55510000-55510600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:55510000-55510600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr15:55510000-55510600	Enhancers	Fetal Kidney	kidney
46	chr15:55510000-55510600	Enhancers	NHLF	lung
47	chr15:55510000-55512000	Enhancers	Stomach Mucosa	stomach
48	chr15:55510000-55512400	Enhancers	Liver	Liver
49	chr15:55510000-55512800	Enhancers	Primary B cells from cord blood	blood
50	chr15:55510200-55510400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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