Variant report

Variant	rs28364485
Chromosome Location	chr15:42693833-42693834
allele	A/G
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	POLR2A	chr15:42693703-42694270	HCT-116	colon:	n/a	n/a
2	HCFC1	chr15:42693827-42694027	K562	blood:	n/a	n/a
3	POLR2A	chr15:42693701-42693906	GM12878	blood:	n/a	n/a
4	NFYB	chr15:42693556-42694338	GM12878	blood:	n/a	chr15:42694017-42694031 chr15:42694019-42694029 chr15:42694016-42694031 chr15:42694018-42694031 chr15:42694016-42694031
5	JUND	chr15:42693797-42694051	K562	blood:	n/a	chr15:42694018-42694027
6	POLR2A	chr15:42693681-42694059	GM12878	blood:	n/a	n/a
7	GABPA	chr15:42693832-42694051	GM12878	blood:	n/a	n/a
8	CBX3	chr15:42693742-42694128	K562	blood:	n/a	n/a
9	POLR2A	chr15:42693700-42694269	GM19193	blood:	n/a	n/a
10	POLR2A	chr15:42693660-42694727	HCT-116	colon:	n/a	n/a
11	RCOR1	chr15:42693769-42694096	K562	blood:	n/a	n/a
12	GABPA	chr15:42693682-42694181	K562	blood:	n/a	n/a
13	POLR2A	chr15:42693763-42693989	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:42693671-42694198	GM12878	blood:	n/a	n/a
15	TCF7L2	chr15:42693756-42694141	HCT-116	colon:	n/a	n/a
16	ELF1	chr15:42693487-42694438	HCT-116	colon:	n/a	n/a
17	GABPA	chr15:42693750-42694128	K562	blood:	n/a	n/a
18	ELF1	chr15:42693729-42694153	K562	blood:	n/a	n/a
19	ELF1	chr15:42693775-42694083	K562	blood:	n/a	n/a
20	TBP	chr15:42693779-42694051	GM12878	blood:	n/a	n/a
21	YY1	chr15:42693763-42694109	HCT-116	colon:	n/a	n/a
22	POLR2A	chr15:42693617-42694162	GM12878	blood:	n/a	n/a
23	BHLHE40	chr15:42693808-42693859	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:42693608-42694273	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42691473..42693889-chr15:42699891..42701622,2	K562	blood:
2	chr15:42692136..42694118-chr15:42750435..42753358,2	K562	blood:

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

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12441027	1.00[MEX][hapmap]
rs1678998	1.00[MEX][hapmap]
rs16973233	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs17592	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17593	1.00[MEX][hapmap]
rs2412694	1.00[MEX][hapmap]
rs2412697	1.00[MEX][hapmap]
rs28364389	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364392	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364395	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364396	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364399	1.00[MEX][hapmap]
rs28364407	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364432	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28364443	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364454	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364496	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28364534	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923941	1.00[MEX][hapmap]
rs4924650	1.00[MEX][hapmap]
rs4924668	1.00[MEX][hapmap]
rs4924669	1.00[MEX][hapmap]
rs4924671	1.00[MEX][hapmap]
rs7167683	1.00[MEX][hapmap]
rs7169432	1.00[AMR][1000 genomes]
rs7176832	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7182306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8028539	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033734	1.00[MEX][hapmap]
rs8037627	1.00[MEX][hapmap]

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:82 , 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	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:42678800-42694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:42678800-42702800	Weak transcription	NHLF	lung
7	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
8	chr15:42679200-42694000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:42680200-42694000	Weak transcription	Left Ventricle	heart
10	chr15:42680200-42696400	Weak transcription	HSMMtube	muscle
11	chr15:42681600-42695400	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:42681800-42694600	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr15:42683800-42704600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:42686200-42694200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr15:42688800-42694400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr15:42689000-42697800	Weak transcription	NHEK	skin
17	chr15:42689000-42712400	Weak transcription	Fetal Brain Male	brain
18	chr15:42689400-42696800	Weak transcription	Psoas Muscle	Psoas
19	chr15:42689400-42703200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:42689800-42706600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr15:42690200-42695600	Strong transcription	Fetal Intestine Small	intestine
22	chr15:42690800-42702400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:42691000-42703000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:42691200-42696000	Strong transcription	Fetal Muscle Leg	muscle
25	chr15:42691200-42696200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr15:42691200-42696400	Strong transcription	Liver	Liver
27	chr15:42691200-42697000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:42691400-42695600	Strong transcription	Fetal Intestine Large	intestine
29	chr15:42691400-42696400	Strong transcription	Primary B cells from cord blood	blood
30	chr15:42691400-42696800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr15:42691400-42697200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:42691600-42695000	Strong transcription	Rectal Smooth Muscle	rectum
33	chr15:42691600-42697400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr15:42692200-42694400	Weak transcription	Pancreas	Pancrea
35	chr15:42692400-42694000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:42692400-42702400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:42692600-42694200	Weak transcription	Brain Substantia Nigra	brain
38	chr15:42692600-42694400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:42692600-42695600	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:42692600-42695800	Weak transcription	Brain Angular Gyrus	brain
41	chr15:42692600-42702400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr15:42692600-42702400	Weak transcription	Aorta	Aorta
43	chr15:42692600-42708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:42692800-42694400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:42692800-42694400	Weak transcription	Brain Anterior Caudate	brain
46	chr15:42692800-42702800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr15:42693200-42695200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:42693200-42697000	Strong transcription	Fetal Stomach	stomach
49	chr15:42693400-42694400	Flanking Active TSS	GM12878-XiMat	blood
50	chr15:42693400-42694600	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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