Variant report

Variant	rs12022928
Chromosome Location	chr1:149994954-149994955
allele	A/G
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	chr1:149994846..149996547-chr1:149998372..149999923,2	K562	blood:
2	chr1:149970593..149972989-chr1:149993853..149996794,2	K562	blood:
3	chr1:149856343..149858353-chr1:149994074..149996091,2	K562	blood:
4	chr1:149993776..149995889-chr1:150021300..150024191,2	MCF-7	breast:
5	chr1:149993826..149996579-chr1:149996891..149998482,2	MCF-7	breast:
6	chr1:149856853..149859922-chr1:149994074..149998027,3	K562	blood:
7	chr1:149990617..149992659-chr1:149993456..149995421,2	K562	blood:
8	chr1:149993912..149996492-chr1:149997463..150000045,2	MCF-7	breast:
9	chr1:149993032..149997672-chr1:150001811..150004898,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184270	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184678	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10494259	0.90[YRI][hapmap]
rs10494260	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11205309	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11205310	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11205312	0.98[ASN][1000 genomes]
rs11205313	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs12023231	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12060171	0.88[AFR][1000 genomes]
rs12060830	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs12064434	0.90[YRI][hapmap]
rs12082035	0.90[YRI][hapmap]
rs12091025	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12091858	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs12409885	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16833063	0.91[YRI][hapmap]
rs16833149	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs16833175	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs16833178	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs16838432	0.90[YRI][hapmap]
rs1868992	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs3738320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3767627	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3767628	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3936952	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4279885	0.91[YRI][hapmap]
rs4926386	0.86[JPT][hapmap]
rs4926400	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs57252299	0.95[ASN][1000 genomes]
rs58342123	0.88[AFR][1000 genomes]
rs58700306	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59054339	0.90[AFR][1000 genomes]
rs61584789	0.98[ASN][1000 genomes]
rs9804143	0.90[YRI][hapmap]
rs9988489	0.91[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149985600-150022000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:149989600-149997800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:149989600-149998000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:149990600-149998000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:149991000-149996000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:149992600-149995000	Enhancers	Stomach Mucosa	stomach
7	chr1:149992800-149995200	Enhancers	Fetal Intestine Large	intestine
8	chr1:149992800-149995200	Enhancers	Fetal Intestine Small	intestine
9	chr1:149993200-149995000	Enhancers	NHEK	skin
10	chr1:149993400-149995000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:149993600-149995000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:149993800-150005400	Weak transcription	Fetal Heart	heart
13	chr1:149994000-149995200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:149994000-149995200	Enhancers	HepG2	liver
15	chr1:149994200-149997200	Weak transcription	Liver	Liver
16	chr1:149994400-149995000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:149994800-149995000	Enhancers	HMEC	breast

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