Variant report

Variant	rs16962666
Chromosome Location	chr15:49918638-49918639
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49918504..49920160-chr15:50344164..50346378,2	MCF-7	breast:
2	chr15:49918122..49920782-chr15:49929071..49931925,2	MCF-7	breast:
3	chr15:49849928..49852326-chr15:49917906..49919869,2	MCF-7	breast:
4	chr15:49917420..49918953-chr15:49923560..49925344,2	K562	blood:
5	chr15:49917069..49919627-chr15:49927874..49930419,3	MCF-7	breast:
6	chr15:49916467..49919057-chr15:49966051..49969032,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104047	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10220770	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10220846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519234	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519235	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519238	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1055135	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11539519	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13313447	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962663	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962664	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962668	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962670	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962676	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962680	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962697	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962735	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1911615	1.00[EUR][1000 genomes]
rs1911618	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58889385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59112029	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59565793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59749619	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59942223	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60640257	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171994	0.87[EUR][1000 genomes]
rs7175199	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7175805	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176887	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391021	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391038	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391046	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406025	1.00[EUR][1000 genomes]
rs73406036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406046	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406069	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406085	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406091	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406098	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406100	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407903	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407904	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407908	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74012439	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74012441	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039808	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041629	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041771	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9652425	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[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	nsv569392	chr15:49789413-49926300	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49913600-49937400	Weak transcription	Spleen	Spleen
2	chr15:49914000-49930000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:49914400-49927200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:49914400-49936400	Weak transcription	Small Intestine	intestine
5	chr15:49914400-49938000	Weak transcription	Brain Substantia Nigra	brain
6	chr15:49914600-49927200	Weak transcription	Fetal Brain Female	brain
7	chr15:49914600-49932600	Weak transcription	Fetal Brain Male	brain
8	chr15:49914600-49934400	Weak transcription	Stomach Mucosa	stomach
9	chr15:49914800-49937800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:49915000-49919600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:49915000-49936600	Weak transcription	Pancreas	Pancrea
12	chr15:49915200-49919600	Weak transcription	Brain Angular Gyrus	brain
13	chr15:49915400-49918800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:49915400-49937800	Weak transcription	Brain Anterior Caudate	brain
15	chr15:49915600-49919800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:49915800-49919800	Weak transcription	Fetal Heart	heart
17	chr15:49916000-49936400	Weak transcription	Psoas Muscle	Psoas
18	chr15:49917000-49918800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:49917200-49920200	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:49917200-49920800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:49917200-49921000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr15:49917400-49918800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:49917400-49918800	ZNF genes & repeats	NHEK	skin
24	chr15:49917600-49920000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:49917800-49919200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:49918000-49919000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr15:49918000-49938600	Weak transcription	Right Ventricle	heart
28	chr15:49918000-49938800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:49918200-49918800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:49918200-49918800	Weak transcription	HSMMtube	muscle
31	chr15:49918200-49919000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:49918200-49919000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:49918200-49919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:49918200-49919000	Weak transcription	NHLF	lung
35	chr15:49918200-49919400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:49918200-49919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:49918200-49919600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:49918200-49919600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:49918200-49919600	Weak transcription	Adipose Nuclei	Adipose
40	chr15:49918200-49919600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr15:49918200-49919600	Weak transcription	Dnd41	blood
42	chr15:49918200-49919600	Weak transcription	K562	blood
43	chr15:49918200-49919800	Weak transcription	Ovary	ovary
44	chr15:49918200-49920400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:49918200-49920800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:49918200-49921000	Weak transcription	Primary T cells from cord blood	blood
47	chr15:49918200-49921000	Enhancers	HMEC	breast
48	chr15:49918200-49921800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:49918200-49922000	Strong transcription	Liver	Liver
50	chr15:49918200-49922800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links