Variant report

Variant	rs16969484
Chromosome Location	chr15:39934458-39934459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39874737..39877413-chr15:39931788..39934836,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10083552	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520145	0.86[ASN][1000 genomes]
rs10520146	0.86[ASN][1000 genomes]
rs10520148	0.86[ASN][1000 genomes]
rs16969307	1.00[EUR][1000 genomes]
rs16969364	1.00[EUR][1000 genomes]
rs16969365	1.00[EUR][1000 genomes]
rs16969384	1.00[EUR][1000 genomes]
rs16969547	0.86[ASN][1000 genomes]
rs16969573	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969678	1.00[ASN][1000 genomes]
rs1994380	0.86[ASN][1000 genomes]
rs2129457	0.86[ASN][1000 genomes]
rs28735552	0.86[ASN][1000 genomes]
rs28785006	0.86[ASN][1000 genomes]
rs34878675	0.86[ASN][1000 genomes]
rs4085744	0.86[ASN][1000 genomes]
rs41376748	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41406047	1.00[EUR][1000 genomes]
rs41515347	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4291886	0.83[ASN][1000 genomes]
rs4322636	1.00[ASN][1000 genomes]
rs4503768	0.86[ASN][1000 genomes]
rs58677957	1.00[EUR][1000 genomes]
rs58716252	1.00[EUR][1000 genomes]
rs59146042	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60228643	0.86[ASN][1000 genomes]
rs61040173	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7163020	1.00[EUR][1000 genomes]
rs7172057	1.00[EUR][1000 genomes]
rs72727029	0.86[ASN][1000 genomes]
rs74008705	1.00[EUR][1000 genomes]
rs8023525	1.00[EUR][1000 genomes]
rs8029417	1.00[EUR][1000 genomes]
rs8030643	1.00[EUR][1000 genomes]
rs8031289	1.00[EUR][1000 genomes]
rs8033803	1.00[EUR][1000 genomes]
rs8035627	1.00[EUR][1000 genomes]
rs8036035	1.00[ASN][1000 genomes]
rs8043342	1.00[EUR][1000 genomes]
rs878941	1.00[EUR][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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:39921400-39937600	Weak transcription	Psoas Muscle	Psoas
3	chr15:39923800-39939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:39931400-39935600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:39931400-39937000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:39932200-39934800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr15:39932200-39935400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:39932600-39934800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:39932600-39935400	Enhancers	HMEC	breast
10	chr15:39932600-39935400	Enhancers	HUVEC	blood vessel
11	chr15:39932800-39934800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:39932800-39935200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:39933000-39935200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:39933000-39935400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:39933000-39936000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr15:39933200-39934600	Weak transcription	Brain Anterior Caudate	brain
17	chr15:39933200-39935400	Enhancers	Colon Smooth Muscle	Colon
18	chr15:39933400-39934800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:39933400-39934800	Flanking Active TSS	NHEK	skin
20	chr15:39933400-39935000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:39933400-39935000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr15:39933400-39935200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr15:39933400-39935400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:39933600-39934600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:39933600-39934800	Enhancers	A549	lung
26	chr15:39933600-39935000	Enhancers	Fetal Heart	heart
27	chr15:39933600-39935000	Enhancers	NHLF	lung
28	chr15:39933600-39935200	Enhancers	NH-A	brain
29	chr15:39933600-39935400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:39933800-39934800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr15:39933800-39934800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:39933800-39934800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr15:39933800-39934800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:39933800-39934800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:39933800-39935200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:39933800-39935200	Enhancers	Rectal Smooth Muscle	rectum
37	chr15:39933800-39935400	Enhancers	NHDF-Ad	bronchial
38	chr15:39933800-39935400	Enhancers	Osteobl	bone
39	chr15:39933800-39937000	Weak transcription	HepG2	liver
40	chr15:39933800-39937800	Enhancers	HSMM	muscle
41	chr15:39934000-39934600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr15:39934000-39934600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:39934000-39934800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:39934000-39934800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr15:39934000-39934800	Enhancers	Stomach Smooth Muscle	stomach
46	chr15:39934000-39935200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:39934000-39936400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:39934000-39937400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:39934200-39934600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr15:39934200-39934600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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