Variant report

Variant	rs668813
Chromosome Location	chr1:179843291-179843292
allele	G/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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179841843..179844701-chr1:179846021..179848651,3	MCF-7	breast:
2	chr1:179842979..179846933-chr1:179922588..179926684,5	K562	blood:
3	chr1:179841983..179844053-chr1:180123561..180126113,2	K562	blood:
4	chr1:179832603..179840385-chr1:179843229..179848672,10	MCF-7	breast:
5	chr1:179843055..179844585-chr12:93321119..93323720,2	MCF-7	breast:
6	chr1:179840648..179843448-chr1:179843849..179845352,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL359853.2-1	chr1:179842841-179845312	NONHSAT008224

No data

Variant related genes	Relation type
ENSG00000169905	Chromatin interaction
ENSG00000258664	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000102189	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1148813	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148814	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148818	0.83[ASN][1000 genomes]
rs1281409	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1281414	0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1281415	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1281419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281424	0.83[ASN][1000 genomes]
rs1281425	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1281431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1290274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1295972	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299683	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299685	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17370666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1758143	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2762857	0.95[ASN][1000 genomes]
rs2777907	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2777916	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2794584	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476280	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs524166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555755	0.89[EUR][1000 genomes]
rs576723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs627897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs651455	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs683812	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv519273	chr1:179831248-179847877	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179820400-179844200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
3	chr1:179826200-179843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:179828000-179845600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:179829800-179844800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:179830200-179845200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:179831200-179845000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:179832400-179844000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:179832400-179844200	Strong transcription	Fetal Thymus	thymus
10	chr1:179834600-179844800	Weak transcription	Fetal Brain Male	brain
11	chr1:179834800-179844000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:179835000-179843400	Weak transcription	Gastric	stomach
13	chr1:179835000-179844800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:179835000-179845600	Weak transcription	Ovary	ovary
15	chr1:179835000-179846400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:179835000-179846400	Weak transcription	Spleen	Spleen
17	chr1:179835200-179845000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:179835200-179845200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:179835200-179845600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:179835400-179846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:179836000-179844800	Weak transcription	HSMMtube	muscle
22	chr1:179836400-179843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:179836400-179844600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:179836600-179844200	Weak transcription	Esophagus	oesophagus
25	chr1:179836600-179845400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:179837000-179845600	Weak transcription	Aorta	Aorta
27	chr1:179837200-179845400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:179837400-179845000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:179837400-179845400	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:179837600-179845600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:179837800-179843400	Weak transcription	NHLF	lung
32	chr1:179838200-179845800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:179838200-179846000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:179838200-179846200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:179838400-179843400	Weak transcription	Fetal Stomach	stomach
36	chr1:179838400-179845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:179838800-179843400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:179838800-179844800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:179839000-179845200	Weak transcription	Fetal Brain Female	brain
40	chr1:179839200-179844000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:179840000-179843400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:179840400-179845600	Weak transcription	Brain Substantia Nigra	brain
43	chr1:179840600-179845000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:179840600-179845200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:179841200-179843800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:179841200-179844000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:179841200-179844200	Strong transcription	HMEC	breast
48	chr1:179841200-179844800	Strong transcription	HSMM	muscle
49	chr1:179841400-179843400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:179841400-179844000	Strong transcription	Primary T cells fromperipheralblood	blood

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