Variant report

Variant	rs12441580
Chromosome Location	chr15:56500473-56500474
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56498392..56501238-chr15:56507855..56509963,2	K562	blood:
2	chr15:56500425..56503148-chr15:56514379..56516558,2	K562	blood:
3	chr15:56499669..56501343-chr15:56501763..56504338,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10444835	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071244	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071248	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071251	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437466	1.00[CEU][hapmap]
rs12438262	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438452	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438525	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438606	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438670	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439033	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439133	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439245	1.00[CEU][hapmap]
rs12440495	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440509	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440898	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441182	1.00[CEU][hapmap]
rs12443028	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443486	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1402173	1.00[CEU][hapmap]
rs16976721	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976722	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976737	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976776	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976787	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976793	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976808	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16976820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976824	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238684	1.00[CEU][hapmap]
rs17819426	1.00[CEU][hapmap]
rs17819450	1.00[CEU][hapmap]
rs2718927	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28895323	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858883	1.00[CEU][hapmap]
rs4310793	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56798454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177904	1.00[CEU][hapmap]
rs7180561	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181011	0.83[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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56453600-56515000	Weak transcription	NHLF	lung
2	chr15:56459200-56511000	Weak transcription	Esophagus	oesophagus
3	chr15:56466000-56514200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:56467000-56511600	Weak transcription	Fetal Intestine Small	intestine
5	chr15:56470800-56503800	Weak transcription	Fetal Lung	lung
6	chr15:56480200-56515400	Weak transcription	Hela-S3	cervix
7	chr15:56485000-56502800	Weak transcription	Gastric	stomach
8	chr15:56485600-56521200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:56489200-56503600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:56493200-56515400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:56495200-56501600	Enhancers	Primary B cells from peripheral blood	blood
12	chr15:56495200-56504400	Weak transcription	Fetal Intestine Large	intestine
13	chr15:56496400-56501200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr15:56496600-56515200	Weak transcription	Left Ventricle	heart
15	chr15:56497000-56502000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr15:56497000-56502600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:56497000-56502600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr15:56497400-56505000	Weak transcription	HSMMtube	muscle
19	chr15:56497600-56500600	Weak transcription	Brain Substantia Nigra	brain
20	chr15:56497600-56501600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr15:56497800-56502400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:56498000-56503800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr15:56498200-56508000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:56498400-56500800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:56498400-56501000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:56498400-56501400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:56498400-56503800	Weak transcription	HepG2	liver
28	chr15:56498400-56504400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:56498400-56514400	Weak transcription	NHEK	skin
30	chr15:56498400-56515200	Weak transcription	HUVEC	blood vessel
31	chr15:56498600-56501800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:56498600-56502600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:56498600-56502600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:56498800-56502800	Enhancers	Dnd41	blood
35	chr15:56499000-56501800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr15:56499200-56502000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:56499200-56502400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr15:56499400-56500600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:56499400-56500800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:56499400-56501600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:56499400-56502600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:56499600-56501800	Flanking Active TSS	GM12878-XiMat	blood
43	chr15:56499800-56500600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr15:56499800-56500600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:56499800-56501200	Enhancers	NH-A	brain
46	chr15:56499800-56502000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr15:56500000-56500600	Enhancers	Aorta	Aorta
48	chr15:56500000-56500600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:56500000-56500600	Enhancers	Ovary	ovary
50	chr15:56500000-56500600	Enhancers	HMEC	breast

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