Variant report

Variant	rs16953967
Chromosome Location	chr15:77836521-77836522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77835384..77837203-chr15:77911255..77913813,2	MCF-7	breast:
2	chr15:77829651..77831982-chr15:77834371..77837022,2	MCF-7	breast:
3	chr15:77835732..77836546-chr15:78113747..78114395,2	MCF-7	breast:
4	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
5	chr15:77795040..77797177-chr15:77834449..77837320,2	MCF-7	breast:
6	chr15:77835652..77836578-chr15:77876310..77876975,3	MCF-7	breast:
7	chr15:77795420..77798597-chr15:77834386..77837370,5	MCF-7	breast:
8	chr15:77827126..77831240-chr15:77834209..77836612,4	K562	blood:
9	chr15:77787983..77789966-chr15:77835290..77836892,2	MCF-7	breast:
10	chr15:77835734..77836523-chr15:77909574..77910418,2	MCF-7	breast:
11	chr15:77789311..77789873-chr15:77836001..77836547,2	K562	blood:

No data

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11855272	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856084	0.88[JPT][hapmap]
rs12324211	0.88[JPT][hapmap]
rs1317320	0.94[JPT][hapmap]
rs16968895	0.94[JPT][hapmap]
rs16968897	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16968900	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16968930	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17394448	0.94[JPT][hapmap]
rs17471480	0.88[JPT][hapmap]
rs17471697	0.87[JPT][hapmap]
rs2137111	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2307141	0.89[JPT][hapmap]
rs28375490	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28534698	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28712147	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784788	0.89[JPT][hapmap]
rs4243046	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61097729	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61483316	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7495653	0.84[ASN][1000 genomes]
rs869302	0.82[ASN][1000 genomes]
rs869310	0.83[ASN][1000 genomes]
rs883627	0.88[JPT][hapmap]
rs907370	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907371	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907398	0.89[JPT][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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16953967	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
2	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:77833000-77836600	Enhancers	Fetal Brain Male	brain
4	chr15:77833800-77843200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:77834000-77841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:77834200-77840800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:77834800-77837200	Enhancers	Gastric	stomach
8	chr15:77835000-77836600	Enhancers	Fetal Heart	heart
9	chr15:77835600-77836800	Active TSS	Primary T cells from cord blood	blood
10	chr15:77835800-77836800	Enhancers	Placenta	Placenta
11	chr15:77835800-77836800	Enhancers	Right Atrium	heart
12	chr15:77835800-77838000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:77835800-77838200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:77836000-77836800	Enhancers	Right Ventricle	heart
15	chr15:77836000-77837200	Enhancers	Fetal Muscle Leg	muscle
16	chr15:77836000-77837800	Weak transcription	HSMMtube	muscle
17	chr15:77836200-77836600	Enhancers	Fetal Intestine Small	intestine
18	chr15:77836200-77836600	Enhancers	Fetal Stomach	stomach
19	chr15:77836200-77836600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr15:77836200-77836800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:77836200-77836800	Enhancers	Pancreas	Pancrea
22	chr15:77836200-77836800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr15:77836200-77836800	Enhancers	Spleen	Spleen
24	chr15:77836200-77837000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:77836200-77837800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:77836200-77837800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:77836200-77837800	Weak transcription	Lung	lung
28	chr15:77836200-77837800	Weak transcription	HSMM	muscle
29	chr15:77836200-77837800	Weak transcription	Osteobl	bone
30	chr15:77836200-77838000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:77836200-77838000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:77836200-77838000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:77836200-77838000	Weak transcription	Left Ventricle	heart
34	chr15:77836200-77838000	Weak transcription	A549	lung
35	chr15:77836200-77838000	Weak transcription	HMEC	breast
36	chr15:77836200-77838000	Weak transcription	NH-A	brain
37	chr15:77836200-77838000	Weak transcription	NHDF-Ad	bronchial
38	chr15:77836200-77838200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:77836200-77838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:77836200-77838200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:77836200-77838200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:77836200-77838200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:77836200-77838200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:77836200-77838200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:77836200-77838200	Weak transcription	Adipose Nuclei	Adipose
46	chr15:77836200-77838400	Weak transcription	HUVEC	blood vessel
47	chr15:77836200-77839000	Enhancers	Stomach Mucosa	stomach
48	chr15:77836200-77839600	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:77836200-77840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr15:77836200-77841000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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