Variant report

Variant	rs28364501
Chromosome Location	chr15:42697135-42697136
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr15:42696781-42697296	K562	blood:	n/a	chr15:42697150-42697159 chr15:42697147-42697160 chr15:42697149-42697158 chr15:42697148-42697157 chr15:42697149-42697158

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:42697094-42697144	ECC-1	luminal epithelium:	n/a
2	chr15:42697094-42697144	NHDF-neo	bronchial:	n/a
3	chr15:42697094-42697144	HUVEC	blood vessel:	n/a
4	chr15:42697094-42697144	AG10803	skin:	n/a
5	chr15:42697094-42697144	HNPCEpiC	eye:	n/a
6	chr15:42697094-42697144	AoSMC	blood vessel:	n/a
7	chr15:42697094-42697144	BE2_C	brain:	n/a
8	chr15:42697094-42697144	GM19239	blood:	n/a
9	chr15:42697094-42697144	HRPEpiC	eye:	n/a
10	chr15:42697094-42697144	BJ	skin:	n/a
11	chr15:42697094-42697144	HIPEpiC	eye:	n/a
12	chr15:42697094-42697144	A549	lung:	n/a
13	chr15:42697094-42697144	HCT-116	colon:	n/a
14	chr15:42697094-42697144	ovcar-3	ovarian:	n/a
15	chr15:42697094-42697144	NH-A	brain:	n/a
16	chr15:42697094-42697144	GM06990	blood:	n/a
17	chr15:42697094-42697144	HRCEpiC	kidney:	n/a
18	chr15:42697094-42697144	K562	blood:	n/a
19	chr15:42697094-42697144	HCF	heart:	n/a
20	chr15:42697094-42697144	HMEC	breast:	n/a
21	chr15:42697094-42697144	HRE	kidney:	n/a
22	chr15:42697094-42697144	GM12892	blood:	n/a
23	chr15:42697094-42697144	SK-N-SH	brain:	n/a
24	chr15:42697094-42697144	Hela-S3	cervix:	n/a
25	chr15:42697094-42697144	HCPEpiC	choroid plexus:	n/a
26	chr15:42697094-42697144	MCF-7	breast:	n/a
27	chr15:42697094-42697144	AG09309	skin:	n/a
28	chr15:42697094-42697144	HPAEpiC	pulmonary alveolar:	n/a
29	chr15:42697094-42697144	SK-N-SH_RA	brain:	n/a
30	chr15:42697094-42697144	PFSK-1	brain:	n/a
31	chr15:42697094-42697144	SAEC	small airway:	n/a
32	chr15:42697094-42697144	PrEC	prostate:	n/a
33	chr15:42697094-42697144	LNCaP	prostate:	n/a
34	chr15:42697094-42697144	PANC-1	pancreas:	n/a
35	chr15:42697094-42697144	HEK293	kidney:	embryo
36	chr15:42697094-42697144	AG09319	gingival:	n/a
37	chr15:42697094-42697144	AG04449	skin:	fetal
38	chr15:42697094-42697144	NHBE	bronchial:	n/a
39	chr15:42697094-42697144	HEEpiC	esophagus:	n/a
40	chr15:42697094-42697144	Caco-2	colon:	n/a
41	chr15:42697094-42697144	HL-60	blood:	n/a
42	chr15:42697094-42697144	HAEpiC	amniotic membrane:	n/a
43	chr15:42697094-42697144	GM12878	blood:	n/a
44	chr15:42697094-42697144	NT2-D1	testis:	n/a
45	chr15:42697094-42697144	U87	brain:	n/a
46	chr15:42697094-42697144	CMK	blood:	n/a
47	chr15:42697094-42697144	ProgFib	skin:	n/a
48	chr15:42697094-42697144	Jurkat	blood:	n/a
49	chr15:42697094-42697144	SK-N-MC	brain:	n/a
50	chr15:42697094-42697144	IMR90	lung:	fetal

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42696812..42699500-chr15:42700218..42703009,3	K562	blood:
2	chr15:42693940..42698488-chr15:42698720..42703314,5	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAPN3-1	chr15:42697025-42697153	NONHSAT042006

No data

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28364401	1.00[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs28364453	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364457	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364459	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364513	0.96[AFR][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:96 , 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	chr15:42689400-42703200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:42689800-42706600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:42690800-42702400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:42691000-42703000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:42691400-42697200	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:42691600-42697400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr15:42692400-42702400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:42692600-42702400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:42692600-42702400	Weak transcription	Aorta	Aorta
18	chr15:42692600-42708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:42692800-42702800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:42693600-42697200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:42693600-42703000	Weak transcription	Brain Germinal Matrix	brain
22	chr15:42693800-42697200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:42694000-42703000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:42694200-42702400	Weak transcription	Placenta	Placenta
25	chr15:42694200-42704000	Weak transcription	Small Intestine	intestine
26	chr15:42694600-42697400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:42694600-42750600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:42694800-42702200	Weak transcription	Thymus	Thymus
29	chr15:42694800-42702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:42694800-42703000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:42694800-42706800	Weak transcription	GM12878-XiMat	blood
32	chr15:42694800-42708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:42695000-42697200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr15:42695000-42699000	Weak transcription	Pancreas	Pancrea
35	chr15:42695000-42702000	Weak transcription	Primary T cells from cord blood	blood
36	chr15:42695000-42702200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:42695000-42702600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:42695000-42703000	Weak transcription	Colonic Mucosa	Colon
39	chr15:42695000-42703000	Weak transcription	HSMM	muscle
40	chr15:42695000-42703200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:42695000-42704000	Weak transcription	HUVEC	blood vessel
42	chr15:42695000-42716000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:42695200-42698400	Weak transcription	Fetal Thymus	thymus
44	chr15:42695200-42698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:42695200-42699000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr15:42695200-42700800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:42695200-42702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:42695200-42702800	Weak transcription	Left Ventricle	heart
49	chr15:42695400-42697200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr15:42695400-42697400	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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