Variant report

Variant	rs6590809
Chromosome Location	chr11:100560519-100560520
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100559088..100560635-chr11:100578926..100581208,2	K562	blood:
2	chr11:100555471..100559429-chr11:100560336..100563382,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165895	Chromatin interaction
ENSG00000248027	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10160451	0.90[ASN][1000 genomes]
rs1021794	0.95[YRI][hapmap]
rs10895006	0.82[AFR][1000 genomes]
rs11224389	0.84[AFR][1000 genomes]
rs6590808	0.82[AFR][1000 genomes]
rs7107791	0.95[YRI][hapmap]
rs7130376	0.83[ASN][1000 genomes]
rs7933751	1.00[ASN][1000 genomes]
rs7947643	0.86[YRI][hapmap]
rs7951366	0.85[ASN][1000 genomes]
rs7951626	0.85[ASN][1000 genomes]
rs7952198	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv556122	chr11:99893282-100585889	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1039852	chr11:99901695-100610533	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv541152	chr11:99901695-100610533	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1043022	chr11:100387466-100610533	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv832246	chr11:100426725-100606957	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6590809	MMP3	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100557200-100560600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:100557400-100560600	Active TSS	Fetal Muscle Trunk	muscle
3	chr11:100557400-100561000	Active TSS	HSMMtube	muscle
4	chr11:100557600-100560600	Active TSS	Fetal Stomach	stomach
5	chr11:100557600-100560600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr11:100557800-100560600	Active TSS	Stomach Smooth Muscle	stomach
7	chr11:100558800-100560600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:100558800-100560600	Weak transcription	Esophagus	oesophagus
9	chr11:100558800-100560800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:100559200-100560600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:100559200-100560600	Weak transcription	Gastric	stomach
12	chr11:100559200-100561200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:100559400-100560600	Active TSS	GM12878-XiMat	blood
14	chr11:100559400-100561000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:100559400-100561000	Enhancers	NHEK	skin
16	chr11:100559400-100562600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:100559400-100563200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:100559400-100564400	Weak transcription	Psoas Muscle	Psoas
19	chr11:100559600-100560600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr11:100559600-100560600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:100559600-100560800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:100559600-100560800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr11:100559800-100560600	Weak transcription	Colonic Mucosa	Colon
24	chr11:100559800-100560600	Enhancers	Fetal Kidney	kidney
25	chr11:100559800-100560800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:100559800-100560800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:100559800-100560800	Enhancers	Dnd41	blood
28	chr11:100559800-100560800	Flanking Active TSS	NHLF	lung
29	chr11:100559800-100561000	Enhancers	Ovary	ovary
30	chr11:100559800-100561000	Enhancers	HMEC	breast
31	chr11:100559800-100562600	Weak transcription	Hela-S3	cervix
32	chr11:100559800-100574600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:100559800-100580000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:100559800-100580000	Weak transcription	HSMM	muscle
35	chr11:100560000-100560600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:100560000-100560600	Active TSS	Lung	lung
37	chr11:100560000-100560800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:100560000-100560800	Enhancers	Adipose Nuclei	Adipose
39	chr11:100560000-100560800	Active TSS	Brain Cingulate Gyrus	brain
40	chr11:100560000-100560800	Enhancers	Pancreas	Pancrea
41	chr11:100560000-100561000	Enhancers	Spleen	Spleen
42	chr11:100560000-100566800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr11:100560200-100560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:100560200-100560600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:100560200-100560600	Enhancers	Liver	Liver
46	chr11:100560200-100560600	Weak transcription	Fetal Intestine Large	intestine
47	chr11:100560200-100560600	Weak transcription	Placenta	Placenta
48	chr11:100560200-100560800	Enhancers	H9 Cell Line	embryonic stem cell
49	chr11:100560200-100560800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:100560200-100560800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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