Variant report

Variant	rs3743988
Chromosome Location	chr16:70766378-70766379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70765832..70768076-chr16:70774273..70775782,2	MCF-7	breast:
2	chr16:70720725..70722557-chr16:70763820..70766425,2	MCF-7	breast:
3	chr16:70719882..70721897-chr16:70765943..70767700,2	K562	blood:
4	chr16:70763729..70766674-chr16:70767583..70772048,4	K562	blood:
5	chr16:70761517..70763051-chr16:70766034..70768582,2	K562	blood:

Variant related genes	Relation type
ENSG00000132613	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10153136	0.89[CHB][hapmap]
rs11864614	0.81[CHB][hapmap]
rs12149236	0.91[ASN][1000 genomes]
rs16970484	0.93[CEU][hapmap]
rs16970513	0.93[CEU][hapmap]
rs17248914	0.93[CEU][hapmap];0.84[MEX][hapmap]
rs17307409	1.00[JPT][hapmap]
rs2290614	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs2902830	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3760118	0.93[CEU][hapmap];0.92[MEX][hapmap]
rs3785421	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3785425	0.89[CHB][hapmap]
rs4985364	0.86[CEU][hapmap];0.84[MEX][hapmap]
rs4985423	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[ASN][1000 genomes]
rs60028268	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499335	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs6499336	0.93[CEU][hapmap]
rs7185187	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7185921	0.93[CEU][hapmap]
rs7188712	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7190561	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7194091	0.93[CEU][hapmap]
rs7196225	0.90[EUR][1000 genomes]
rs7202363	0.86[CEU][hapmap]
rs7203578	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7205738	0.84[ASN][1000 genomes]
rs8060947	0.86[CEU][hapmap]
rs9939763	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]

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	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1059226	chr16:70708698-70779144	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
9	nsv906889	chr16:70724001-70790831	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv906890	chr16:70740707-70790831	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1061191	chr16:70754975-71201367	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3743988	NQO1	cis	parietal	SCAN
rs3743988	TPPP3	cis	parietal	SCAN
rs3743988	CENPT	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70727000-70770800	Weak transcription	GM12878-XiMat	blood
2	chr16:70750400-70767000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:70750600-70766600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr16:70750800-70771800	Weak transcription	A549	lung
5	chr16:70752600-70770800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr16:70753200-70766400	Strong transcription	Primary T cells from cord blood	blood
7	chr16:70753400-70767200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr16:70754200-70768800	Weak transcription	Osteobl	bone
9	chr16:70754400-70776600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr16:70754400-70780000	Weak transcription	Hela-S3	cervix
11	chr16:70755200-70769600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:70755600-70774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr16:70755800-70772000	Weak transcription	Small Intestine	intestine
14	chr16:70756600-70768600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr16:70758400-70768800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr16:70759000-70766400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr16:70759000-70766400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:70759800-70766400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr16:70759800-70769600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr16:70759800-70770400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr16:70760000-70769000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr16:70760000-70784200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr16:70760200-70766400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr16:70760400-70766800	Weak transcription	HUVEC	blood vessel
25	chr16:70760600-70771000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr16:70760800-70769400	Weak transcription	Fetal Kidney	kidney
27	chr16:70761000-70769400	Weak transcription	Stomach Mucosa	stomach
28	chr16:70761200-70768600	Weak transcription	NHDF-Ad	bronchial
29	chr16:70761200-70768800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr16:70761200-70777600	Weak transcription	K562	blood
31	chr16:70761800-70768800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr16:70762200-70768800	Weak transcription	Right Ventricle	heart
33	chr16:70762200-70769400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr16:70762200-70778200	Weak transcription	Ovary	ovary
35	chr16:70762400-70779600	Weak transcription	Aorta	Aorta
36	chr16:70762600-70766800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr16:70762600-70770400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr16:70762600-70774600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr16:70762800-70769400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr16:70763200-70767200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr16:70763200-70771000	Weak transcription	Gastric	stomach
42	chr16:70763400-70773000	Weak transcription	Fetal Brain Female	brain
43	chr16:70764000-70766400	Enhancers	Left Ventricle	heart
44	chr16:70764400-70767400	Weak transcription	Fetal Brain Male	brain
45	chr16:70764400-70769200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:70764400-70771000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:70764800-70766600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr16:70764800-70766600	Strong transcription	Primary B cells from cord blood	blood
49	chr16:70764800-70766600	Enhancers	HMEC	breast
50	chr16:70764800-70769200	Weak transcription	Fetal Lung	lung

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