Variant report

Variant	rs9649397
Chromosome Location	chr7:116567710-116567711
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:116567075..116568820-chr7:116569252..116572115,2	MCF-7	breast:
2	chr7:116562838..116565216-chr7:116567059..116569364,3	K562	blood:
3	chr7:116562487..116565467-chr7:116567653..116570595,2	MCF-7	breast:
4	chr7:116565598..116568288-chr7:116594057..116596980,2	MCF-7	breast:
5	chr7:116557404..116561072-chr7:116567108..116571328,4	K562	blood:
6	chr7:116563032..116565216-chr7:116567059..116570510,3	K562	blood:

Variant related genes	Relation type
ENSG00000004866	Chromatin interaction
ENSG00000227199	Chromatin interaction
ENSG00000214188	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11977452	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12537143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12665999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12666016	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13312052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2074025	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2214168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6947485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7778381	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7800249	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7802605	0.89[JPT][hapmap]
rs7803820	0.85[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs7807976	0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs9649395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9649396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9791495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv889074	chr7:116552859-116604194	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv889075	chr7:116552859-116610237	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv889073	chr7:116552859-116611113	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9649397	MET	cis	Artery Aorta	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116544000-116568600	Weak transcription	Fetal Brain Male	brain
2	chr7:116544400-116570600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:116552000-116570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:116552400-116569000	Weak transcription	NHLF	lung
5	chr7:116553200-116570600	Weak transcription	Brain Substantia Nigra	brain
6	chr7:116555400-116568800	Weak transcription	Gastric	stomach
7	chr7:116555400-116570400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:116556800-116570600	Weak transcription	Aorta	Aorta
9	chr7:116557000-116570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:116557000-116570800	Weak transcription	NHEK	skin
11	chr7:116558000-116570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:116558000-116570600	Weak transcription	Lung	lung
13	chr7:116558000-116570800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:116558200-116570400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:116558200-116570400	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:116558200-116570600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:116558200-116570800	Weak transcription	HMEC	breast
18	chr7:116558400-116568400	Weak transcription	HepG2	liver
19	chr7:116558400-116570600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:116558400-116570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:116558400-116570600	Weak transcription	Brain Anterior Caudate	brain
22	chr7:116558400-116570800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr7:116558600-116570400	Weak transcription	Fetal Lung	lung
24	chr7:116558600-116570600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:116558800-116570400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:116558800-116570400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:116559000-116570200	Weak transcription	Placenta	Placenta
28	chr7:116559000-116570400	Weak transcription	Dnd41	blood
29	chr7:116559000-116570400	Weak transcription	Hela-S3	cervix
30	chr7:116559200-116570600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:116559200-116570600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:116559200-116570600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:116559200-116576000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:116559400-116567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:116559600-116570400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr7:116559600-116570400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr7:116559600-116570600	Weak transcription	GM12878-XiMat	blood
38	chr7:116559600-116570800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:116559600-116570800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:116559600-116570800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:116560800-116570600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:116560800-116570600	Weak transcription	Liver	Liver
43	chr7:116561000-116570200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr7:116561000-116570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:116561200-116570400	Weak transcription	A549	lung
46	chr7:116561200-116570600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr7:116561200-116570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:116561400-116570000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr7:116562400-116567800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:116562400-116570600	Weak transcription	HUVEC	blood vessel

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