Variant report

Variant	rs12028640
Chromosome Location	chr1:48226939-48226940
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-543D5.3.1-2	chr1:48226804-48226952	ENSG00000223814

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12040464	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12045022	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12085966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4927044	0.91[CEU][hapmap];0.85[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829760	chr1:48111126-48308188	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv871257	chr1:48111699-48334490	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv871175	chr1:48150309-48254782	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001126	chr1:48164622-48320862	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1003161	chr1:48207715-48286563	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:48215400-48236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:48218600-48228400	Weak transcription	Lung	lung
3	chr1:48218600-48239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:48222400-48231800	Weak transcription	Pancreas	Pancrea
5	chr1:48224400-48228200	Weak transcription	Esophagus	oesophagus
6	chr1:48224400-48230400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:48225400-48231600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:48225400-48234000	Enhancers	Right Atrium	heart
9	chr1:48225600-48230000	Weak transcription	Fetal Intestine Small	intestine
10	chr1:48225600-48237000	Weak transcription	Fetal Intestine Large	intestine
11	chr1:48225800-48228600	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:48226000-48227200	Enhancers	Fetal Muscle Leg	muscle
13	chr1:48226400-48227000	Bivalent Enhancer	Fetal Stomach	stomach
14	chr1:48226400-48228200	Enhancers	Spleen	Spleen
15	chr1:48226600-48227000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:48226600-48227000	Enhancers	Hela-S3	cervix
17	chr1:48226600-48227200	Enhancers	Aorta	Aorta
18	chr1:48226600-48227600	Enhancers	Fetal Lung	lung
19	chr1:48226600-48227600	Enhancers	Placenta	Placenta
20	chr1:48226600-48231600	Weak transcription	Brain Germinal Matrix	brain
21	chr1:48226800-48228600	Enhancers	GM12878-XiMat	blood

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