Variant report

Variant	rs16976824
Chromosome Location	chr15:56496716-56496717
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56492206..56494642-chr15:56495488..56498069,2	MCF-7	breast:
2	chr15:56494171..56496972-chr15:56541763..56543619,2	K562	blood:
3	chr15:56495337..56498069-chr15:56534935..56537509,2	K562	blood:

Variant related genes	Relation type
ENSG00000181827	Chromatin interaction
ENSG00000151575	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10444835	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071244	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071248	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071251	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071256	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437466	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12438262	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438452	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438525	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438606	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438670	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439033	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439133	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439245	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12440495	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440509	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440898	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441182	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12441580	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443028	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443087	0.82[CEU][hapmap]
rs12443486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1402173	1.00[CEU][hapmap]
rs16976721	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976722	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976737	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976776	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976787	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976793	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976808	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16976820	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238684	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17819426	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17819450	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2718927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28895323	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858883	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4310793	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56798454	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177904	1.00[CEU][hapmap]
rs7180561	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181011	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv528965	chr15:56489159-56504598	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 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	chr15:56453600-56515000	Weak transcription	NHLF	lung
2	chr15:56457400-56500400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:56459200-56511000	Weak transcription	Esophagus	oesophagus
4	chr15:56464600-56497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:56466000-56497000	Weak transcription	HSMMtube	muscle
6	chr15:56466000-56500000	Weak transcription	Thymus	Thymus
7	chr15:56466000-56514200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:56467000-56500400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:56467000-56511600	Weak transcription	Fetal Intestine Small	intestine
10	chr15:56470200-56498800	Weak transcription	Dnd41	blood
11	chr15:56470800-56503800	Weak transcription	Fetal Lung	lung
12	chr15:56477000-56500400	Weak transcription	Liver	Liver
13	chr15:56477200-56497000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:56480000-56500000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:56480200-56497000	Weak transcription	HUVEC	blood vessel
16	chr15:56480200-56515400	Weak transcription	Hela-S3	cervix
17	chr15:56481400-56497800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:56482600-56497000	Weak transcription	NH-A	brain
19	chr15:56482600-56500200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:56484800-56500000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:56485000-56502800	Weak transcription	Gastric	stomach
22	chr15:56485600-56500000	Weak transcription	Aorta	Aorta
23	chr15:56485600-56521200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:56486600-56497000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:56488200-56497000	Weak transcription	HSMM	muscle
26	chr15:56488400-56496800	Weak transcription	Fetal Brain Male	brain
27	chr15:56489200-56497200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:56489200-56503600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:56490600-56497400	Weak transcription	HepG2	liver
30	chr15:56490800-56497000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:56491600-56497000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:56491600-56497400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:56492000-56496800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:56492200-56497200	Weak transcription	A549	lung
35	chr15:56492400-56497400	Weak transcription	Primary T cells from cord blood	blood
36	chr15:56493000-56500000	Weak transcription	Ovary	ovary
37	chr15:56493200-56515400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:56493600-56497600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:56494800-56497200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:56494800-56497400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:56495000-56496800	Enhancers	K562	blood
42	chr15:56495000-56500000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:56495200-56497200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:56495200-56500000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:56495200-56500000	Weak transcription	Psoas Muscle	Psoas
46	chr15:56495200-56501600	Enhancers	Primary B cells from peripheral blood	blood
47	chr15:56495200-56504400	Weak transcription	Fetal Intestine Large	intestine
48	chr15:56495400-56497000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:56495400-56497000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:56495400-56497200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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