Variant report

Variant	rs9940308
Chromosome Location	chr16:12388443-12388444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12388084..12390009-chr16:12417985..12420361,2	MCF-7	breast:
2	chr16:12387753..12389838-chr16:12389944..12391563,2	MCF-7	breast:
3	chr16:12381810..12383489-chr16:12387831..12390561,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238685	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1032887	0.91[ASN][1000 genomes]
rs10500380	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13332306	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13380622	0.83[ASN][1000 genomes]
rs16959078	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16959080	0.83[ASN][1000 genomes]
rs16959097	0.91[ASN][1000 genomes]
rs16959100	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16959126	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16959130	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16959350	1.00[CEU][hapmap]
rs2271269	0.83[ASN][1000 genomes]
rs28408454	0.83[ASN][1000 genomes]
rs41325045	1.00[JPT][hapmap]
rs60280624	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6498273	0.83[ASN][1000 genomes]
rs7187929	0.83[ASN][1000 genomes]
rs7189091	0.83[ASN][1000 genomes]
rs73506137	0.96[AMR][1000 genomes]
rs8058627	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8062145	0.83[ASN][1000 genomes]
rs870641	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs905948	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9926796	1.00[CEU][hapmap]
rs9927344	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9929445	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9932158	1.00[CEU][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	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12323400-12394200	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr16:12338200-12396200	Weak transcription	Thymus	Thymus
3	chr16:12347800-12395200	Weak transcription	Right Ventricle	heart
4	chr16:12356000-12390200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr16:12359800-12418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
7	chr16:12372800-12393800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:12373400-12414200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr16:12373600-12396600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr16:12374000-12389400	Weak transcription	HSMMtube	muscle
11	chr16:12374000-12397400	Weak transcription	Ovary	ovary
12	chr16:12374200-12417200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr16:12383200-12407800	Weak transcription	Gastric	stomach
14	chr16:12384000-12390800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr16:12384000-12394600	Weak transcription	Lung	lung
16	chr16:12384200-12389000	Weak transcription	NHEK	skin
17	chr16:12384200-12389200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:12384200-12394600	Weak transcription	Spleen	Spleen
19	chr16:12384400-12409000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr16:12385000-12394400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr16:12385000-12394400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr16:12385000-12394600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr16:12385000-12396400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr16:12385200-12394400	Weak transcription	Adipose Nuclei	Adipose
25	chr16:12385400-12399200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr16:12385800-12389200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:12385800-12410800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:12386400-12401600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr16:12387000-12389600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr16:12387200-12388600	Enhancers	HepG2	liver
31	chr16:12387200-12388800	Strong transcription	Primary B cells from cord blood	blood
32	chr16:12387600-12390600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:12387800-12390600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr16:12387800-12392200	Strong transcription	Primary T cells from cord blood	blood
35	chr16:12388000-12388600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr16:12388000-12388600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr16:12388000-12388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr16:12388000-12398600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr16:12388200-12393200	Weak transcription	Fetal Heart	heart
40	chr16:12388400-12388600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:12388400-12388600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr16:12388400-12388600	Enhancers	Left Ventricle	heart
43	chr16:12388400-12388800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr16:12388400-12388800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr16:12388400-12388800	Weak transcription	Esophagus	oesophagus
46	chr16:12388400-12389200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr16:12388400-12389200	Enhancers	Right Atrium	heart
48	chr16:12388400-12389400	Enhancers	GM12878-XiMat	blood
49	chr16:12388400-12389600	Enhancers	HUVEC	blood vessel
50	chr16:12388400-12389800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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