Variant report

Variant	rs11646288
Chromosome Location	chr16:82769476-82769477
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	chr16:82762397..82764526-chr16:82767820..82769912,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1000076	0.85[ASN][1000 genomes]
rs1000078	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10438615	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10438616	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10438634	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10514557	0.82[ASN][1000 genomes]
rs10514558	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10514559	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs11150492	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1157118	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs11646321	0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs11647530	0.89[ASN][1000 genomes]
rs12103370	0.85[JPT][hapmap]
rs12448904	0.87[CHB][hapmap];0.82[JPT][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13332390	0.85[YRI][hapmap]
rs13334499	1.00[YRI][hapmap]
rs1350888	0.81[JPT][hapmap]
rs1350889	0.81[JPT][hapmap]
rs1462035	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1462037	0.87[CHB][hapmap];0.91[ASN][1000 genomes]
rs1462043	1.00[JPT][hapmap]
rs17183029	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17183071	0.85[ASN][1000 genomes]
rs17183279	0.87[ASN][1000 genomes]
rs17183490	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17273696	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs17274555	0.87[ASN][1000 genomes]
rs17274597	0.81[JPT][hapmap]
rs17274793	0.88[ASN][1000 genomes]
rs17274905	0.87[ASN][1000 genomes]
rs2126369	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2318186	0.87[ASN][1000 genomes]
rs2318187	0.87[ASN][1000 genomes]
rs2318190	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs28374534	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4238723	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4293370	0.89[ASN][1000 genomes]
rs4559899	0.80[ASN][1000 genomes]
rs4620944	0.93[ASN][1000 genomes]
rs4783262	0.92[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4783263	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs4783266	1.00[JPT][hapmap]
rs55713633	0.86[ASN][1000 genomes]
rs58786779	0.88[ASN][1000 genomes]
rs62034474	0.87[ASN][1000 genomes]
rs62034479	0.88[ASN][1000 genomes]
rs62034480	0.89[ASN][1000 genomes]
rs62034481	0.89[ASN][1000 genomes]
rs62034482	0.89[ASN][1000 genomes]
rs62034484	0.90[ASN][1000 genomes]
rs7185447	0.85[ASN][1000 genomes]
rs7197336	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7197344	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7197523	0.87[ASN][1000 genomes]
rs7201087	0.87[ASN][1000 genomes]
rs8044955	1.00[JPT][hapmap]
rs8046067	0.84[ASN][1000 genomes]
rs8046098	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8060282	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057341	chr16:82363800-83198907	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv542997	chr16:82363800-83198907	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1059718	chr16:82564054-82810003	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv573379	chr16:82713551-82887631	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
7	esv2751616	chr16:82714696-82852296	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1067216	chr16:82719694-82821762	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
9	nsv543000	chr16:82719694-82821762	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1064438	chr16:82762729-82788901	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv907026	chr16:82765607-82812853	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82750200-82780600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr16:82762000-82773800	Weak transcription	NHEK	skin
3	chr16:82766600-82770600	Enhancers	Aorta	Aorta
4	chr16:82766600-82770600	Enhancers	Left Ventricle	heart
5	chr16:82766800-82788600	Weak transcription	HMEC	breast
6	chr16:82767400-82770800	Enhancers	Fetal Brain Male	brain
7	chr16:82767600-82771000	Enhancers	Fetal Muscle Leg	muscle
8	chr16:82767800-82769600	Enhancers	Right Ventricle	heart
9	chr16:82767800-82771000	Enhancers	Fetal Stomach	stomach
10	chr16:82768000-82771200	Enhancers	Brain Germinal Matrix	brain
11	chr16:82768200-82770200	Enhancers	Fetal Brain Female	brain
12	chr16:82768200-82771000	Enhancers	HSMMtube	muscle
13	chr16:82768400-82769800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr16:82768400-82771000	Enhancers	Colon Smooth Muscle	Colon
15	chr16:82768600-82769800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr16:82768600-82769800	Enhancers	HSMM	muscle
17	chr16:82768600-82770000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:82768600-82770000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr16:82768600-82770200	Enhancers	NHDF-Ad	bronchial
20	chr16:82768600-82770400	Weak transcription	Psoas Muscle	Psoas
21	chr16:82768600-82770800	Enhancers	Rectal Smooth Muscle	rectum
22	chr16:82768600-82773400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:82768600-82775800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr16:82768600-82784800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr16:82768800-82769600	Enhancers	Brain Angular Gyrus	brain
26	chr16:82768800-82769600	Enhancers	Brain Substantia Nigra	brain
27	chr16:82768800-82770600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr16:82768800-82770600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr16:82769000-82769800	Flanking Active TSS	Fetal Heart	heart
30	chr16:82769000-82770000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr16:82769000-82770600	Enhancers	Primary B cells from peripheral blood	blood
32	chr16:82769200-82769800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr16:82769200-82769800	Enhancers	NHLF	lung
34	chr16:82769200-82769800	Flanking Active TSS	Osteobl	bone
35	chr16:82769200-82770000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr16:82769200-82770200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr16:82769200-82770200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr16:82769200-82785200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr16:82769400-82769800	Active TSS	Brain Hippocampus Middle	brain
40	chr16:82769400-82770000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr16:82769400-82770200	Enhancers	GM12878-XiMat	blood

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