Variant report

Variant	rs1468242
Chromosome Location	chr7:79798624-79798625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10230368	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[ASN][1000 genomes]
rs10257372	0.91[ASN][1000 genomes]
rs10272499	0.94[ASW][hapmap];0.84[CEU][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10277707	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12671775	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12706673	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2428466	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2428467	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523192	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2714457	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714460	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4512317	0.88[CEU][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6945280	0.94[ASW][hapmap];0.84[CEU][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6956455	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7808119	0.88[CEU][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][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	nsv429785	chr7:79589749-80177049	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1468242	HGF	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79781200-79803200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:79783800-79806600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:79786200-79799600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:79788600-79799000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:79788600-79799800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:79789400-79814200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:79791200-79799400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:79791600-79801400	Weak transcription	Ovary	ovary
9	chr7:79791800-79799000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:79792200-79799000	Weak transcription	Gastric	stomach
11	chr7:79792800-79809000	Weak transcription	Fetal Kidney	kidney
12	chr7:79793200-79799600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:79793200-79802000	Weak transcription	Brain Angular Gyrus	brain
14	chr7:79794400-79802200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:79795000-79799200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:79795400-79816000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:79795600-79809000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:79796400-79816000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:79796600-79802000	Weak transcription	Brain Substantia Nigra	brain
20	chr7:79796800-79799000	Weak transcription	Fetal Lung	lung
21	chr7:79796800-79801600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:79796800-79802200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:79797200-79799400	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:79797600-79801600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:79798400-79802600	ZNF genes & repeats	A549	lung

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