Variant report

Variant	rs2994985
Chromosome Location	chr1:241649184-241649185
allele	C/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:241130395..241130952-chr1:241648617..241649469,2	MCF-7	breast:
2	chr1:241051044..241051957-chr1:241649144..241649909,2	MCF-7	breast:
3	chr1:241643115..241646158-chr1:241648871..241651877,3	K562	blood:
4	chr1:241051464..241052000-chr1:241648987..241649656,3	K562	blood:
5	chr1:241646443..241651437-chr1:241651445..241654937,7	K562	blood:
6	chr1:241474594..241475098-chr1:241648774..241649668,2	MCF-7	breast:
7	chr1:241648420..241650338-chr1:241682166..241684882,2	K562	blood:
8	chr1:241474385..241475055-chr1:241648747..241649435,2	MCF-7	breast:
9	chr1:241576862..241577389-chr1:241648832..241649350,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000091483	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12071124	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12120348	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1335898	0.85[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2153694	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2225788	0.87[EUR][1000 genomes]
rs2992644	0.85[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2994982	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2994987	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2994989	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]
rs4659607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4660100	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6678766	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7530270	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:30 , 50 per page) page: 1

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	chr1:241644200-241649800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:241644600-241649600	Enhancers	NHLF	lung
5	chr1:241644600-241657200	Weak transcription	Right Ventricle	heart
6	chr1:241646400-241657200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:241647000-241649200	Enhancers	NHDF-Ad	bronchial
8	chr1:241647000-241649400	Enhancers	HUVEC	blood vessel
9	chr1:241647000-241649800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:241647000-241656400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:241647000-241656800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:241647000-241657000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:241647000-241657000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:241647000-241657200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:241647000-241657400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:241647000-241657600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:241647000-241657600	Weak transcription	HMEC	breast
18	chr1:241647000-241657600	Weak transcription	NH-A	brain
19	chr1:241647000-241657600	Weak transcription	NHEK	skin
20	chr1:241647000-241660000	Weak transcription	A549	lung
21	chr1:241647000-241660000	Weak transcription	Hela-S3	cervix
22	chr1:241647000-241666600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:241647200-241650600	Enhancers	K562	blood
24	chr1:241647400-241657200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:241647600-241657000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:241647600-241657600	Weak transcription	HSMM	muscle
27	chr1:241648200-241649600	Enhancers	GM12878-XiMat	blood
28	chr1:241648400-241660200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:241649000-241657400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:241649000-241657400	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links