Variant report

Variant	rs1277343
Chromosome Location	chr6:24401238-24401239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:24400637-24401262	K562	blood:	n/a	n/a
2	MYC	chr6:24401067-24401248	H1-hESC	embryonic stem cell:	n/a	n/a
3	ATF1	chr6:24400774-24401240	K562	blood:	n/a	n/a
4	POLR2A	chr6:24399949-24401532	H1-hESC	embryonic stem cell:	n/a	n/a
5	EP300	chr6:24400606-24401411	K562	blood:	n/a	n/a
6	MAX	chr6:24400903-24401307	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr6:24400786-24401267	K562	blood:	n/a	n/a
8	NR2F2	chr6:24400347-24401359	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:24398649..24401531-chr6:24495303..24497005,2	K562	blood:
2	chr6:24399777..24402402-chr6:24720450..24723229,2	MCF-7	breast:
3	chr6:24398527..24401443-chr6:24402320..24404718,2	MCF-7	breast:
4	chr6:24400135..24402578-chr6:24776210..24779187,2	K562	blood:

No data

Variant related genes	Relation type
MRS2	TF binding region
ENSG00000112312	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000124532	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1056283	0.95[ASN][1000 genomes]
rs1321819	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13735	0.92[ASN][1000 genomes]
rs1742280	0.80[ASN][1000 genomes]
rs1742282	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1772253	0.84[ASN][1000 genomes]
rs2753922	0.84[ASN][1000 genomes]
rs2793422	0.84[ASN][1000 genomes]
rs2876672	0.84[ASN][1000 genomes]
rs3827640	0.92[ASN][1000 genomes]
rs6456612	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6920147	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6936856	0.81[ASN][1000 genomes]
rs7769012	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793652	0.90[ASN][1000 genomes]
rs793654	0.84[ASN][1000 genomes]
rs793657	0.86[ASN][1000 genomes]
rs793679	0.83[ASN][1000 genomes]
rs793680	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793682	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793684	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793686	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793687	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793688	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793690	0.80[ASN][1000 genomes]
rs9393554	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1277343	MRS2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24399600-24401800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr6:24400200-24402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:24400400-24401800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:24400600-24402400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:24400600-24402800	Enhancers	K562	blood
6	chr6:24401000-24401800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:24401000-24402400	Enhancers	HepG2	liver
8	chr6:24401000-24402600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:24401000-24402600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:24401000-24402800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:24401200-24401400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:24401200-24401400	Enhancers	Fetal Kidney	kidney
13	chr6:24401200-24401400	Enhancers	NHEK	skin
14	chr6:24401200-24401600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:24401200-24401800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:24401200-24402000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:24401200-24402600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr6:24401200-24402600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:24401200-24402600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:24401200-24402600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:24401200-24402600	Enhancers	Hela-S3	cervix
22	chr6:24401200-24402800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:24401200-24402800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:24401200-24402800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:24401200-24402800	Enhancers	Fetal Intestine Large	intestine
26	chr6:24401200-24402800	Enhancers	Placenta	Placenta
27	chr6:24401200-24403000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr6:24401200-24403000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links