Variant report

Variant	rs6945280
Chromosome Location	chr7:79818716-79818717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10230368	0.89[MEX][hapmap]
rs10238438	0.81[GIH][hapmap]
rs10248616	0.81[ASW][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs10256687	0.81[ASW][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap]
rs10272499	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277707	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11767465	0.81[ASW][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap]
rs12671775	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706673	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1468242	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]
rs2428466	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2428467	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2523184	0.84[CEU][hapmap];0.80[CHB][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2523192	0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2714457	0.81[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2714460	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4458811	0.81[EUR][1000 genomes]
rs4512317	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4610665	0.81[EUR][1000 genomes]
rs6956455	0.88[ASW][hapmap];0.84[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6980300	0.93[CHB][hapmap]
rs7808119	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][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
rs6945280	HGF	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79801800-79840400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:79802600-79820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:79807200-79829200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:79807200-79833400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:79807800-79842000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr7:79809600-79847600	Weak transcription	HUVEC	blood vessel
7	chr7:79811600-79845000	Weak transcription	Primary T cells from cord blood	blood
8	chr7:79812400-79827800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:79812400-79827800	Weak transcription	NHEK	skin
10	chr7:79812400-79828200	Weak transcription	HMEC	breast
11	chr7:79813200-79818800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:79813400-79829000	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:79813800-79828000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:79814200-79820400	Weak transcription	Left Ventricle	heart
15	chr7:79814200-79842600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:79814600-79819200	Enhancers	Fetal Brain Male	brain
17	chr7:79815000-79830600	Weak transcription	Placenta	Placenta
18	chr7:79815000-79848200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:79815000-79850200	Weak transcription	Lung	lung
20	chr7:79815200-79859600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:79815600-79819200	Enhancers	Liver	Liver
22	chr7:79816000-79819000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:79816200-79846800	Weak transcription	Esophagus	oesophagus
24	chr7:79816400-79819200	Enhancers	Brain Angular Gyrus	brain
25	chr7:79816400-79854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:79816600-79826000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr7:79816800-79820400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:79816800-79830600	Weak transcription	Gastric	stomach
29	chr7:79816800-79831800	Weak transcription	Hela-S3	cervix
30	chr7:79817000-79819200	Enhancers	Brain Substantia Nigra	brain
31	chr7:79817000-79819400	Enhancers	Fetal Lung	lung
32	chr7:79817000-79819600	Enhancers	Brain Cingulate Gyrus	brain
33	chr7:79817000-79820000	Weak transcription	A549	lung
34	chr7:79817000-79820400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:79817000-79821000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:79817000-79826600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:79817000-79828000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:79817000-79828600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:79817000-79829800	Weak transcription	Osteobl	bone
40	chr7:79817000-79830600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:79817000-79833000	Weak transcription	HSMM	muscle
42	chr7:79817000-79841000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:79817000-79842400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:79817000-79851200	Weak transcription	Aorta	Aorta
45	chr7:79817200-79819200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr7:79817200-79819600	Enhancers	Brain Anterior Caudate	brain
47	chr7:79817200-79820000	Weak transcription	NHLF	lung
48	chr7:79817200-79820600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr7:79817200-79825200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:79817200-79825200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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