Variant report

Variant	rs16842078
Chromosome Location	chr1:223927746-223927747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223891443..223896975-chr1:223925207..223929791,6	MCF-7	breast:
2	chr1:223926311..223927941-chr1:223933092..223935068,2	K562	blood:
3	chr1:223900203..223902153-chr1:223927273..223928993,2	K562	blood:
4	chr1:223900203..223901722-chr1:223926667..223928773,2	K562	blood:
5	chr1:223898969..223903164-chr1:223924094..223928992,8	MCF-7	breast:
6	chr1:223918635..223922245-chr1:223925850..223929641,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10158199	1.00[EUR][1000 genomes]
rs10158508	1.00[EUR][1000 genomes]
rs10158843	1.00[EUR][1000 genomes]
rs10159010	1.00[EUR][1000 genomes]
rs1153962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153966	1.00[EUR][1000 genomes]
rs12025911	1.00[EUR][1000 genomes]
rs12026548	1.00[EUR][1000 genomes]
rs12027762	1.00[EUR][1000 genomes]
rs12040996	1.00[EUR][1000 genomes]
rs12047952	1.00[EUR][1000 genomes]
rs1222131	1.00[EUR][1000 genomes]
rs12239402	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239445	1.00[EUR][1000 genomes]
rs12239678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375296	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs16842173	1.00[EUR][1000 genomes]
rs16842177	1.00[EUR][1000 genomes]
rs16842201	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs16842217	1.00[EUR][1000 genomes]
rs16842234	1.00[EUR][1000 genomes]
rs16842259	1.00[EUR][1000 genomes]
rs16842291	1.00[EUR][1000 genomes]
rs16842341	1.00[EUR][1000 genomes]
rs1890119	1.00[EUR][1000 genomes]
rs2230082	1.00[EUR][1000 genomes]
rs28370064	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28370079	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28370099	1.00[EUR][1000 genomes]
rs28370160	1.00[EUR][1000 genomes]
rs28370161	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs28370162	1.00[EUR][1000 genomes]
rs28458390	1.00[EUR][1000 genomes]
rs28684725	1.00[EUR][1000 genomes]
rs41345146	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs55760211	0.86[AFR][1000 genomes]
rs56947789	1.00[EUR][1000 genomes]
rs57380389	1.00[EUR][1000 genomes]
rs58753599	1.00[EUR][1000 genomes]
rs59433589	1.00[EUR][1000 genomes]
rs59793743	1.00[EUR][1000 genomes]
rs59948383	1.00[EUR][1000 genomes]
rs59970447	1.00[EUR][1000 genomes]
rs73114413	1.00[EUR][1000 genomes]
rs73125398	1.00[EUR][1000 genomes]
rs73127405	1.00[EUR][1000 genomes]
rs73127411	1.00[EUR][1000 genomes]
rs73127438	1.00[EUR][1000 genomes]
rs73127450	1.00[EUR][1000 genomes]
rs747811	1.00[EUR][1000 genomes]
rs7515215	1.00[EUR][1000 genomes]
rs9286986	1.00[EUR][1000 genomes]
rs9970756	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
7	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:223919800-223931200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:223921200-223927800	Genic enhancers	A549	lung
11	chr1:223921200-223932800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:223921400-223931400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:223921600-223932800	Weak transcription	Liver	Liver
15	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:223921800-223933400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
21	chr1:223922400-223927800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:223922600-223928000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:223922800-223928600	Weak transcription	Fetal Thymus	thymus
24	chr1:223922800-223930600	Weak transcription	Spleen	Spleen
25	chr1:223922800-223930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:223922800-223931600	Weak transcription	Brain Germinal Matrix	brain
27	chr1:223922800-223934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:223923000-223928600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:223923000-223931800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:223923200-223928000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:223923200-223928200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:223923800-223929400	Genic enhancers	NHEK	skin
33	chr1:223924200-223928000	Enhancers	Stomach Smooth Muscle	stomach
34	chr1:223924400-223928000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:223924800-223928400	Enhancers	Aorta	Aorta
36	chr1:223924800-223929800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr1:223925200-223934600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:223925400-223927800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:223925400-223930600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:223925400-223930800	Weak transcription	Gastric	stomach
41	chr1:223925400-223931800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:223925400-223931800	Weak transcription	Ovary	ovary
43	chr1:223925400-223934800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:223925600-223929800	Genic enhancers	HMEC	breast
45	chr1:223925800-223929000	Enhancers	Fetal Kidney	kidney
46	chr1:223926000-223927800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:223926000-223927800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:223926000-223927800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:223926000-223928000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:223926000-223928000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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