Variant report

Variant	rs28364500
Chromosome Location	chr15:42696606-42696607
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr15:42696436-42696859	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42693940..42698488-chr15:42698720..42703314,5	K562	blood:

Variant related genes	Relation type
CAPN3	TF binding region
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs11070367	1.00[EUR][1000 genomes]
rs11070371	1.00[EUR][1000 genomes]
rs11633276	1.00[EUR][1000 genomes]
rs11856807	1.00[EUR][1000 genomes]
rs12102204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12324205	0.94[ASN][1000 genomes]
rs12593511	1.00[EUR][1000 genomes]
rs12902924	1.00[EUR][1000 genomes]
rs12911561	1.00[EUR][1000 genomes]
rs1659214	1.00[EUR][1000 genomes]
rs1659216	1.00[EUR][1000 genomes]
rs1659220	1.00[EUR][1000 genomes]
rs1659223	1.00[EUR][1000 genomes]
rs1659225	1.00[EUR][1000 genomes]
rs1871156	1.00[EUR][1000 genomes]
rs2244773	1.00[EUR][1000 genomes]
rs2289293	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289297	1.00[EUR][1000 genomes]
rs2412675	1.00[EUR][1000 genomes]
rs2412676	1.00[EUR][1000 genomes]
rs2412678	1.00[EUR][1000 genomes]
rs2412683	1.00[EUR][1000 genomes]
rs2412684	1.00[EUR][1000 genomes]
rs2412689	1.00[EUR][1000 genomes]
rs2412694	1.00[EUR][1000 genomes]
rs2412695	1.00[EUR][1000 genomes]
rs2412716	1.00[EUR][1000 genomes]
rs2578651	1.00[EUR][1000 genomes]
rs2595935	1.00[EUR][1000 genomes]
rs2620372	1.00[EUR][1000 genomes]
rs28364379	1.00[EUR][1000 genomes]
rs28364398	1.00[EUR][1000 genomes]
rs28364400	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28364462	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364475	1.00[ASN][1000 genomes]
rs28364491	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364495	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364498	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364503	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364504	1.00[EUR][1000 genomes]
rs28364507	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28364509	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28364511	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28364519	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28364522	1.00[EUR][1000 genomes]
rs28364523	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28364524	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28364526	1.00[EUR][1000 genomes]
rs28364536	0.94[ASN][1000 genomes]
rs28364540	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28364541	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28364544	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28364557	1.00[EUR][1000 genomes]
rs28489155	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28621687	1.00[EUR][1000 genomes]
rs28745879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899044	1.00[EUR][1000 genomes]
rs2899058	1.00[EUR][1000 genomes]
rs3743002	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4556762	1.00[EUR][1000 genomes]
rs4923936	1.00[EUR][1000 genomes]
rs4923937	1.00[EUR][1000 genomes]
rs4923939	1.00[EUR][1000 genomes]
rs4924640	1.00[EUR][1000 genomes]
rs4924641	1.00[EUR][1000 genomes]
rs4924642	1.00[EUR][1000 genomes]
rs4924643	1.00[EUR][1000 genomes]
rs4924649	1.00[EUR][1000 genomes]
rs4924657	1.00[EUR][1000 genomes]
rs4924670	1.00[EUR][1000 genomes]
rs5028173	1.00[EUR][1000 genomes]
rs5029919	0.94[ASN][1000 genomes]
rs6493024	1.00[EUR][1000 genomes]
rs6493026	1.00[EUR][1000 genomes]
rs6493031	1.00[EUR][1000 genomes]
rs6493034	1.00[EUR][1000 genomes]
rs6493038	1.00[EUR][1000 genomes]
rs6493041	1.00[EUR][1000 genomes]
rs6493047	1.00[EUR][1000 genomes]
rs6493051	1.00[EUR][1000 genomes]
rs655704	1.00[EUR][1000 genomes]
rs67384392	1.00[EUR][1000 genomes]
rs7161982	1.00[EUR][1000 genomes]
rs7164196	1.00[EUR][1000 genomes]
rs7164484	1.00[EUR][1000 genomes]
rs7169553	1.00[EUR][1000 genomes]
rs7169941	0.83[AMR][1000 genomes]
rs7170943	1.00[EUR][1000 genomes]
rs7177193	1.00[EUR][1000 genomes]
rs7177463	1.00[EUR][1000 genomes]
rs7177521	1.00[EUR][1000 genomes]
rs7178396	1.00[EUR][1000 genomes]
rs7181940	1.00[EUR][1000 genomes]
rs7182777	1.00[EUR][1000 genomes]
rs7183399	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183843	1.00[EUR][1000 genomes]
rs8023568	1.00[EUR][1000 genomes]
rs8023678	1.00[EUR][1000 genomes]
rs8036149	1.00[EUR][1000 genomes]
rs8036163	1.00[EUR][1000 genomes]
rs8040720	1.00[EUR][1000 genomes]
rs8042603	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8043033	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs936603	1.00[EUR][1000 genomes]
rs9920851	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:42678800-42702800	Weak transcription	NHLF	lung
5	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
6	chr15:42683800-42704600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr15:42689000-42697800	Weak transcription	NHEK	skin
8	chr15:42689000-42712400	Weak transcription	Fetal Brain Male	brain
9	chr15:42689400-42696800	Weak transcription	Psoas Muscle	Psoas
10	chr15:42689400-42703200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:42689800-42706600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:42690800-42702400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:42691000-42703000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:42691200-42697000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:42691400-42696800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr15:42691400-42697200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:42691600-42697400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr15:42692400-42702400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:42692600-42702400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:42692600-42702400	Weak transcription	Aorta	Aorta
21	chr15:42692600-42708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:42692800-42702800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:42693200-42697000	Strong transcription	Fetal Stomach	stomach
24	chr15:42693600-42697000	Strong transcription	Adipose Nuclei	Adipose
25	chr15:42693600-42697200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:42693600-42703000	Weak transcription	Brain Germinal Matrix	brain
27	chr15:42693800-42696800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:42693800-42696800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:42693800-42697000	Strong transcription	Lung	lung
30	chr15:42693800-42697000	Strong transcription	Right Ventricle	heart
31	chr15:42693800-42697200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:42694000-42696800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:42694000-42703000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:42694200-42702400	Weak transcription	Placenta	Placenta
35	chr15:42694200-42704000	Weak transcription	Small Intestine	intestine
36	chr15:42694400-42696800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:42694600-42697400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:42694600-42750600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:42694800-42702200	Weak transcription	Thymus	Thymus
40	chr15:42694800-42702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:42694800-42703000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:42694800-42706800	Weak transcription	GM12878-XiMat	blood
43	chr15:42694800-42708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:42695000-42697200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:42695000-42699000	Weak transcription	Pancreas	Pancrea
46	chr15:42695000-42702000	Weak transcription	Primary T cells from cord blood	blood
47	chr15:42695000-42702200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:42695000-42702600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:42695000-42703000	Weak transcription	Colonic Mucosa	Colon
50	chr15:42695000-42703000	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links