Variant report

Variant	rs16969445
Chromosome Location	chr15:39922387-39922388
allele	A/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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:39921577..39922712-chr15:39960446..39961289,4	MCF-7	breast:
2	chr15:39871401..39883645-chr15:39918779..39926575,24	MCF-7	breast:
3	chr15:39872729..39875575-chr15:39921037..39923866,5	MCF-7	breast:
4	chr15:39921577..39922481-chr15:39960668..39961289,3	MCF-7	breast:
5	chr15:39603952..39606127-chr15:39921042..39922610,2	MCF-7	breast:
6	chr15:39921354..39922952-chr3:64065874..64067555,2	MCF-7	breast:
7	chr15:39909459..39912628-chr15:39921888..39923922,3	MCF-7	breast:
8	chr15:39920700..39923129-chr15:39958970..39962199,4	MCF-7	breast:
9	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
10	chr15:39890030..39893862-chr15:39920684..39923175,4	MCF-7	breast:
11	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
12	chr15:39922048..39922709-chr15:39960306..39961692,3	MCF-7	breast:
13	chr15:39921225..39923942-chr15:39930395..39933053,2	MCF-7	breast:
14	chr15:39884252..39886366-chr15:39922051..39924260,2	MCF-7	breast:
15	chr15:39921489..39922463-chr15:39960386..39961014,2	MCF-7	breast:
16	chr15:39904208..39905755-chr15:39920256..39923195,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1004739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004741	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520135	0.85[CEU][hapmap]
rs10520137	1.00[CEU][hapmap]
rs11070220	0.88[CEU][hapmap]
rs11070222	1.00[CEU][hapmap]
rs11070223	0.86[CEU][hapmap]
rs11070225	0.88[CEU][hapmap]
rs1134485	1.00[CEU][hapmap]
rs11630406	0.88[CEU][hapmap]
rs11631570	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11632879	0.88[CEU][hapmap]
rs11633974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11635103	0.88[CEU][hapmap]
rs11638041	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11638500	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11852591	0.88[CEU][hapmap]
rs11852649	0.88[CEU][hapmap]
rs11854797	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs11856294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856448	0.88[CHB][hapmap]
rs11856971	0.85[CEU][hapmap]
rs11857819	0.85[CEU][hapmap]
rs11857927	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908846	1.00[CEU][hapmap]
rs12912082	1.00[CEU][hapmap]
rs16969386	1.00[CEU][hapmap]
rs16969410	0.88[CEU][hapmap]
rs16969459	0.88[CEU][hapmap]
rs16969460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969475	1.00[CEU][hapmap]
rs16969478	1.00[CEU][hapmap]
rs16969495	0.83[CHB][hapmap]
rs16969637	0.88[CHB][hapmap]
rs16969640	0.88[CHB][hapmap]
rs1876853	1.00[CEU][hapmap]
rs2228261	1.00[CEU][hapmap]
rs2292305	1.00[CEU][hapmap]
rs2411312	0.84[EUR][1000 genomes]
rs2411313	0.88[CEU][hapmap]
rs2412409	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412410	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412411	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412413	1.00[CEU][hapmap]
rs2412415	0.88[CEU][hapmap]
rs2412417	0.88[CEU][hapmap]
rs2412419	1.00[CEU][hapmap]
rs2898686	0.88[CEU][hapmap]
rs2898687	1.00[CEU][hapmap]
rs2898688	0.88[CEU][hapmap]
rs34275067	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35754803	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784390	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4349120	0.88[CEU][hapmap]
rs4476147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547308	0.88[CEU][hapmap]
rs4583211	0.88[CEU][hapmap]
rs56722485	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57969006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58332880	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60884629	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7162070	1.00[CEU][hapmap]
rs7162781	1.00[CEU][hapmap]
rs7167184	1.00[CEU][hapmap]
rs7168755	0.88[CEU][hapmap]
rs7169478	1.00[CEU][hapmap]
rs7169574	0.88[CEU][hapmap]
rs72725045	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs753599	0.88[CEU][hapmap]
rs8029602	1.00[CEU][hapmap]
rs8032035	0.88[CEU][hapmap]
rs8036376	0.86[CEU][hapmap]
rs884584	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39913200-39924000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:39913400-39922400	Enhancers	Fetal Intestine Large	intestine
3	chr15:39913400-39923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:39914000-39922800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:39914200-39922600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr15:39914600-39922800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:39914600-39923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr15:39914600-39923600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr15:39914600-39923800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr15:39914800-39923800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr15:39916000-39924000	Enhancers	HMEC	breast
12	chr15:39916200-39923400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:39917400-39923800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:39917600-39926200	Weak transcription	Esophagus	oesophagus
16	chr15:39918800-39923400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:39919400-39922400	Enhancers	Duodenum Mucosa	Duodenum
18	chr15:39919400-39922600	Enhancers	Fetal Lung	lung
19	chr15:39919400-39922600	Enhancers	GM12878-XiMat	blood
20	chr15:39919400-39923000	Enhancers	Fetal Brain Male	brain
21	chr15:39920000-39923400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr15:39920000-39923600	Enhancers	HUVEC	blood vessel
23	chr15:39920000-39924400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:39920200-39922800	Enhancers	Fetal Thymus	thymus
25	chr15:39920200-39924400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:39920600-39922400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:39920600-39924200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:39920800-39922800	Enhancers	Primary T cells from cord blood	blood
29	chr15:39920800-39924400	Enhancers	NHEK	skin
30	chr15:39920800-39925200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:39921000-39922400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr15:39921000-39922800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr15:39921200-39922400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:39921200-39923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:39921200-39924400	Enhancers	Fetal Heart	heart
36	chr15:39921400-39922400	Enhancers	Fetal Brain Female	brain
37	chr15:39921400-39924400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:39921400-39926200	Weak transcription	Pancreas	Pancrea
39	chr15:39921400-39937600	Weak transcription	Psoas Muscle	Psoas
40	chr15:39921600-39922600	Weak transcription	Colonic Mucosa	Colon
41	chr15:39921600-39923200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:39921600-39924000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:39921800-39923000	Weak transcription	Right Ventricle	heart
44	chr15:39921800-39923000	Weak transcription	HSMMtube	muscle
45	chr15:39921800-39923200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:39922000-39922400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:39922000-39922400	Enhancers	Fetal Kidney	kidney
48	chr15:39922000-39922400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr15:39922000-39923000	Weak transcription	Small Intestine	intestine
50	chr15:39922000-39923400	Weak transcription	Osteobl	bone

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