Variant report

Variant	rs9393553
Chromosome Location	chr6:24401654-24401655
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:24401608-24402114	HepG2	liver:	n/a	n/a
2	TEAD4	chr6:24401620-24402108	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr6:24401560-24401881	HepG2	liver:	n/a	chr6:24401704-24401713
4	JUN	chr6:24401578-24401822	HepG2	liver:	n/a	chr6:24401703-24401716 chr6:24401704-24401713
5	POLR2A	chr6:24401543-24404415	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24399777..24402402-chr6:24720450..24723229,2	MCF-7	breast:
2	chr6:24400135..24402578-chr6:24776210..24779187,2	K562	blood:

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

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12055519	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1321820	0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2273605	0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs2298062	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3761789	0.91[ASN][1000 genomes]
rs6942189	0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs9393555	0.91[ASN][1000 genomes]
rs9393556	0.81[CHB][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9393553	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs9393553	HIST1H2BF	cis	cerebellum	SCAN
rs9393553	ZSCAN12	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr6:24401200-24401800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:24401200-24402000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:24401200-24402600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr6:24401200-24402600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:24401200-24402600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:24401200-24402600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:24401200-24402600	Enhancers	Hela-S3	cervix
18	chr6:24401200-24402800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:24401200-24402800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:24401200-24402800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:24401200-24402800	Enhancers	Fetal Intestine Large	intestine
22	chr6:24401200-24402800	Enhancers	Placenta	Placenta
23	chr6:24401200-24403000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr6:24401200-24403000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:24401400-24401800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:24401400-24402400	Weak transcription	Fetal Kidney	kidney
27	chr6:24401400-24402400	Weak transcription	NHEK	skin
28	chr6:24401400-24402600	Enhancers	Ovary	ovary
29	chr6:24401600-24402200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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