Variant report

Variant	rs34702040
Chromosome Location	chr1:159928219-159928220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr1:159927714-159928229	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr1:159927613-159928248	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr1:159927541-159928294	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr1:159927494-159928251	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr1:159927675-159928282	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr1:159927750-159928248	T-47D	breast:	n/a	n/a
7	RCOR1	chr1:159927526-159928222	K562	blood:	n/a	n/a
8	CCNT2	chr1:159927634-159928259	K562	blood:	n/a	n/a
9	GATA1	chr1:159927211-159928332	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:159926244..159929298-chr1:159931208..159934136,4	K562	blood:
2	chr1:159914406..159916851-chr1:159926521..159929440,2	MCF-7	breast:
3	chr1:159922806..159924393-chr1:159927902..159929423,2	MCF-7	breast:
4	chr1:159894586..159896290-chr1:159926599..159929253,2	K562	blood:
5	chr1:159913973..159917644-chr1:159927852..159934070,11	MCF-7	breast:

No data

Variant related genes	Relation type
LINC01133	TF binding region
SLAMF9	TF binding region
ENSG00000085552	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000162723	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12065741	0.87[ASN][1000 genomes]
rs12144158	1.00[ASN][1000 genomes]
rs12732517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12740563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759403	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789426	1.00[ASN][1000 genomes]
rs2840590	0.87[ASN][1000 genomes]
rs34128710	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34401812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35541552	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622571	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35769623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36082532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41265747	0.87[ASN][1000 genomes]
rs58872353	0.87[ASN][1000 genomes]
rs59673346	0.87[ASN][1000 genomes]
rs60537025	0.87[ASN][1000 genomes]
rs61734538	0.87[ASN][1000 genomes]
rs71628158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71628159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71628161	1.00[AMR][1000 genomes]
rs71628162	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71628163	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520773	chr1:159922959-159935569	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
2	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:159924000-159928800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:159924000-159928800	Weak transcription	Esophagus	oesophagus
5	chr1:159924200-159928400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:159924400-159929200	Weak transcription	Osteobl	bone
7	chr1:159925200-159929600	Weak transcription	NHDF-Ad	bronchial
8	chr1:159925400-159929000	Weak transcription	HMEC	breast
9	chr1:159926400-159928800	Weak transcription	NHEK	skin
10	chr1:159927200-159929600	Enhancers	Fetal Intestine Small	intestine
11	chr1:159927600-159930000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:159927600-159930400	Enhancers	Stomach Mucosa	stomach
13	chr1:159927800-159928600	Enhancers	GM12878-XiMat	blood
14	chr1:159927800-159929000	Enhancers	Gastric	stomach
15	chr1:159927800-159929200	Enhancers	Fetal Intestine Large	intestine
16	chr1:159927800-159929800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:159928000-159928600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:159928000-159928800	Weak transcription	Small Intestine	intestine
19	chr1:159928000-159929000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:159928000-159929000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:159928000-159929000	Weak transcription	Lung	lung
22	chr1:159928000-159929000	Weak transcription	Pancreas	Pancrea
23	chr1:159928000-159929200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:159928000-159931000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:159928000-159931800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:159928000-159941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:159928200-159931400	Enhancers	K562	blood

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