Variant report

Variant	rs1055565
Chromosome Location	chr1:211605697-211605698
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:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:211504123..211506416-chr1:211604400..211606288,2	K562	blood:
2	chr1:211556090..211557781-chr1:211604466..211606047,2	K562	blood:
3	chr1:211599016..211601630-chr1:211604235..211606553,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF5-1	chr1:211605661-211605878	ENSG00000153363
2	lnc-TRAF5-1	chr1:211605661-211605877	NONHSAT009289
3	lnc-TRAF5-1	chr1:211605661-211605911	NONHSAT009292
4	lnc-TRAF5-1	chr1:211605661-211606029	NONHSAT009294

No data

Variant related genes	Relation type
ENSG00000153363	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10449313	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1084981	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863888	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[TSI][hapmap]
rs10863895	0.87[ASN][1000 genomes]
rs11580084	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs11811405	0.81[CEU][hapmap]
rs12027724	0.96[CEU][hapmap]
rs12116749	0.96[CEU][hapmap]
rs12118279	0.81[CEU][hapmap]
rs1533217	0.92[CEU][hapmap]
rs1663522	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1777827	0.86[ASN][1000 genomes]
rs2063569	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798559	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920908	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920911	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002258	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3111257	0.81[CEU][hapmap]
rs3111258	0.81[CEU][hapmap]
rs3738199	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3767377	0.96[CEU][hapmap]
rs3767378	0.96[CEU][hapmap]
rs4406705	0.96[CEU][hapmap]
rs4951520	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs4951523	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs6689078	0.80[CEU][hapmap]
rs6700747	0.81[CEU][hapmap]
rs7520989	0.96[CEU][hapmap]
rs7550702	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs784369	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs784379	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs784382	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs784383	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs784385	0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs784389	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1824154	chr1:211565640-211614280	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	nsv945612	chr1:211593276-211615726	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1055565	C1orf74	cis	parietal	SCAN
rs1055565	LAMB3	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211581400-211608200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:211589600-211608800	Weak transcription	GM12878-XiMat	blood
3	chr1:211590400-211607200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:211590400-211607600	Weak transcription	Left Ventricle	heart
5	chr1:211590400-211609000	Weak transcription	Primary B cells from cord blood	blood
6	chr1:211591000-211607400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:211594800-211605800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:211594800-211606200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:211594800-211607200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:211594800-211608400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:211595400-211605800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:211596400-211609200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:211597800-211607800	Weak transcription	Ovary	ovary
14	chr1:211600600-211608000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:211603000-211606400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:211604800-211608800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:211604800-211614800	Weak transcription	Gastric	stomach
18	chr1:211605000-211607800	Weak transcription	Adipose Nuclei	Adipose
19	chr1:211605400-211608000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:211605400-211608200	Weak transcription	Fetal Intestine Large	intestine
21	chr1:211605600-211606200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:211605600-211606400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:211605600-211607400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:211605600-211607400	Strong transcription	Fetal Intestine Small	intestine

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