Variant report

Variant	rs9593134
Chromosome Location	chr13:76425153-76425154
allele	A/G
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	MAX	chr13:76425065-76425435	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr13:76425110-76425389	K562	blood:	n/a	n/a
3	USF1	chr13:76425132-76425322	HepG2	liver:	n/a	chr13:76425253-76425264
4	USF1	chr13:76425049-76425369	H1-hESC	embryonic stem cell:	n/a	chr13:76425253-76425264
5	E2F6	chr13:76425141-76425317	K562	blood:	n/a	n/a
6	POLR2A	chr13:76424932-76425428	Hela-S3	cervix:	n/a	n/a
7	MAX	chr13:76425131-76425328	K562	blood:	n/a	n/a
8	POLR2A	chr13:76425139-76425647	HepG2	liver:	n/a	n/a
9	USF1	chr13:76424994-76425443	ECC-1	luminal epithelium:	n/a	chr13:76425253-76425264
10	USF1	chr13:76425134-76425429	SK-N-SH	brain:	n/a	chr13:76425253-76425264
11	POLR2A	chr13:76425136-76425418	ProgFib	skin:	n/a	n/a
12	USF2	chr13:76425144-76425397	Hela-S3	cervix:	n/a	chr13:76425253-76425264
13	MAX	chr13:76425038-76425337	K562	blood:	n/a	n/a
14	USF1	chr13:76425079-76425404	K562	blood:	n/a	chr13:76425253-76425264
15	USF1	chr13:76425066-76425389	K562	blood:	n/a	chr13:76425253-76425264
16	MAX	chr13:76425006-76425487	ECC-1	luminal epithelium:	n/a	n/a
17	USF1	chr13:76425018-76425345	ECC-1	luminal epithelium:	n/a	chr13:76425253-76425264
18	USF1	chr13:76425140-76425359	H1-hESC	embryonic stem cell:	n/a	chr13:76425253-76425264

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76425109..76426616-chr13:76428342..76430833,2	K562	blood:

Variant related genes	Relation type
LMO7	TF binding region
ENSG00000136153	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12859511	0.87[EUR][1000 genomes]
rs2273996	0.80[YRI][hapmap]
rs7335875	0.89[GIH][hapmap]
rs7996791	0.83[YRI][hapmap]
rs8001647	0.87[EUR][1000 genomes]
rs9318379	0.89[EUR][1000 genomes]
rs9530473	0.86[YRI][hapmap]
rs9573671	0.80[AFR][1000 genomes]
rs9600563	0.80[LWK][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9593134	LMO7	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76387800-76427200	Weak transcription	Ovary	ovary
2	chr13:76391200-76431600	Strong transcription	Hela-S3	cervix
3	chr13:76394400-76435800	Weak transcription	Colon Smooth Muscle	Colon
4	chr13:76396400-76432000	Weak transcription	Brain Substantia Nigra	brain
5	chr13:76396400-76436800	Weak transcription	Fetal Brain Male	brain
6	chr13:76399000-76433200	Weak transcription	Small Intestine	intestine
7	chr13:76399800-76433000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:76400800-76428400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:76406000-76428600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:76406000-76429600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr13:76406000-76430600	Strong transcription	Osteobl	bone
12	chr13:76406000-76436800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr13:76406600-76435000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr13:76406800-76427800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:76408400-76435000	Strong transcription	HSMMtube	muscle
16	chr13:76408400-76435200	Strong transcription	NH-A	brain
17	chr13:76413200-76436800	Strong transcription	NHDF-Ad	bronchial
18	chr13:76413800-76437600	Strong transcription	HSMM	muscle
19	chr13:76414000-76433000	Strong transcription	Liver	Liver
20	chr13:76414200-76433400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr13:76414400-76426200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr13:76414400-76435200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:76414800-76425400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:76415400-76429200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr13:76416000-76426800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr13:76416400-76425200	Weak transcription	Lung	lung
27	chr13:76416400-76434600	Weak transcription	Spleen	Spleen
28	chr13:76416600-76426400	Weak transcription	HUVEC	blood vessel
29	chr13:76416600-76429800	Weak transcription	Stomach Mucosa	stomach
30	chr13:76417200-76427200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr13:76417200-76427200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr13:76417400-76427400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:76417400-76429200	Weak transcription	Adipose Nuclei	Adipose
34	chr13:76417400-76431000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr13:76417400-76433000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr13:76417400-76434600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:76417400-76443800	Weak transcription	Fetal Brain Female	brain
38	chr13:76417600-76427000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr13:76417600-76427200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr13:76417600-76427200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:76417600-76427200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr13:76417600-76427200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:76417600-76427200	Weak transcription	Fetal Stomach	stomach
44	chr13:76417600-76427400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr13:76417600-76427400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr13:76417600-76431400	Weak transcription	Brain Angular Gyrus	brain
47	chr13:76417600-76432600	Weak transcription	Brain Hippocampus Middle	brain
48	chr13:76417600-76434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:76417600-76436800	Weak transcription	Psoas Muscle	Psoas
50	chr13:76417600-76437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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