Variant report

Variant	rs2994989
Chromosome Location	chr1:241656685-241656686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241655894..241658438-chr1:241663957..241666444,2	K562	blood:
2	chr1:241654504..241656882-chr1:241679445..241682289,2	K562	blood:
3	chr1:241653862..241656906-chr1:241669771..241671642,4	K562	blood:
4	chr1:241655533..241657251-chr1:241681709..241683858,2	MCF-7	breast:
5	chr1:241655406..241657552-chr1:241670142..241672034,2	K562	blood:
6	chr1:241626870..241629867-chr1:241656513..241658810,2	K562	blood:

Variant related genes	Relation type
ENSG00000091483	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12071124	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12120348	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1335898	0.84[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2153694	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2225788	0.87[EUR][1000 genomes]
rs2992644	0.84[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2994982	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2994985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994987	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4659607	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4660100	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678766	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7530270	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv527805	chr1:241651018-241656685	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 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	chr1:241639000-241657000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:241643800-241657800	Weak transcription	Psoas Muscle	Psoas
3	chr1:241644600-241657200	Weak transcription	Right Ventricle	heart
4	chr1:241646400-241657200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:241647000-241656800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:241647000-241657000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:241647000-241657000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:241647000-241657200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:241647000-241657400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:241647000-241657600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:241647000-241657600	Weak transcription	HMEC	breast
12	chr1:241647000-241657600	Weak transcription	NH-A	brain
13	chr1:241647000-241657600	Weak transcription	NHEK	skin
14	chr1:241647000-241660000	Weak transcription	A549	lung
15	chr1:241647000-241660000	Weak transcription	Hela-S3	cervix
16	chr1:241647000-241666600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:241647400-241657200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:241647600-241657000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:241647600-241657600	Weak transcription	HSMM	muscle
20	chr1:241648400-241660200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:241649000-241657400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:241649000-241657400	Weak transcription	Osteobl	bone
23	chr1:241649200-241658600	Weak transcription	NHDF-Ad	bronchial
24	chr1:241649400-241657400	Weak transcription	HUVEC	blood vessel
25	chr1:241649600-241657400	Weak transcription	NHLF	lung
26	chr1:241649800-241656800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:241650400-241657400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:241650400-241657400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:241650600-241657400	Weak transcription	K562	blood
30	chr1:241651400-241657000	Weak transcription	Fetal Thymus	thymus
31	chr1:241651600-241657200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:241652000-241665200	Weak transcription	Brain Germinal Matrix	brain
33	chr1:241652400-241659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:241653800-241657400	Weak transcription	Primary B cells from cord blood	blood
35	chr1:241654000-241656800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:241654000-241657600	Weak transcription	Gastric	stomach
37	chr1:241654200-241657200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:241654200-241657200	Weak transcription	Fetal Lung	lung
39	chr1:241654200-241657200	Weak transcription	Thymus	Thymus
40	chr1:241654200-241657600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:241654200-241659200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:241654400-241656800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:241654400-241657200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:241654400-241659200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:241654600-241657600	Weak transcription	HSMMtube	muscle
46	chr1:241655000-241656800	Weak transcription	Primary T cells from cord blood	blood
47	chr1:241655000-241657000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:241655000-241657600	Weak transcription	Placenta	Placenta
49	chr1:241655000-241657800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:241655000-241657800	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links