Variant report

Variant	rs16976787
Chromosome Location	chr15:56461431-56461432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56460981..56464277-chr15:56465842..56468866,3	K562	blood:
2	chr15:56459962..56461531-chr15:56468857..56470997,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10444835	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071244	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071248	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071251	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071256	0.97[AMR][1000 genomes];0.95[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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438452	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438525	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438606	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438670	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439033	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439133	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440495	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440509	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440898	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441580	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443028	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1402173	1.00[CEU][hapmap]
rs16976721	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976722	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976737	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976776	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976793	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976808	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16976820	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976824	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238684	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2718927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28895323	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56798454	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180561	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7181011	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1811079	chr15:56448125-56462293	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56433800-56464000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:56435400-56462400	Weak transcription	Fetal Thymus	thymus
3	chr15:56435400-56465200	Weak transcription	Thymus	Thymus
4	chr15:56442000-56462600	Weak transcription	HSMM	muscle
5	chr15:56442600-56470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:56442800-56462600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:56443200-56462600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:56446600-56468400	Weak transcription	Fetal Lung	lung
9	chr15:56453000-56463200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:56453000-56479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:56453200-56462000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:56453200-56465000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:56453400-56463400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:56453600-56515000	Weak transcription	NHLF	lung
15	chr15:56453800-56463000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:56454000-56462800	Weak transcription	Brain Germinal Matrix	brain
17	chr15:56454000-56464600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:56454200-56465000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:56454400-56462600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:56454400-56462600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:56454400-56462600	Weak transcription	A549	lung
22	chr15:56454400-56463000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:56454400-56464200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:56454400-56465000	Weak transcription	Fetal Stomach	stomach
25	chr15:56454400-56465600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:56454400-56466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:56454400-56467000	Weak transcription	Brain Angular Gyrus	brain
28	chr15:56454400-56467200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:56454400-56470000	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:56454400-56470200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:56454400-56473400	Weak transcription	K562	blood
32	chr15:56454600-56463400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:56454600-56463400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:56454600-56465600	Weak transcription	Brain Substantia Nigra	brain
35	chr15:56454600-56484000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:56454800-56465200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:56455400-56462400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:56456000-56463400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:56456200-56462800	Weak transcription	Liver	Liver
40	chr15:56456600-56464800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr15:56456600-56484800	Weak transcription	Aorta	Aorta
42	chr15:56456800-56463600	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:56457200-56469000	Weak transcription	Hela-S3	cervix
44	chr15:56457400-56465000	Weak transcription	Fetal Intestine Small	intestine
45	chr15:56457400-56500400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:56457800-56462600	Weak transcription	Fetal Intestine Large	intestine
47	chr15:56457800-56463000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:56457800-56471600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:56458000-56470200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr15:56458000-56474000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links