Variant report

Variant	rs6956455
Chromosome Location	chr7:79814927-79814928
allele	A/G
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];1.00[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs10257372	0.89[ASN][1000 genomes]
rs10272499	0.88[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10277707	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12671775	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12706673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468242	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]
rs2428466	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2428467	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523192	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714457	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2714460	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4512317	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6945280	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]
rs7808119	0.88[CEU][hapmap];0.81[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[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
rs6956455	HGF	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79795400-79816000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:79796400-79816000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:79801800-79840400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:79802600-79820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:79806000-79816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:79807200-79829200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:79807200-79833400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:79807600-79816200	Weak transcription	Osteobl	bone
9	chr7:79807800-79816000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:79807800-79842000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:79809400-79815600	Weak transcription	Liver	Liver
12	chr7:79809600-79847600	Weak transcription	HUVEC	blood vessel
13	chr7:79809800-79815400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr7:79810000-79815800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:79810200-79816000	Weak transcription	Fetal Brain Female	brain
16	chr7:79810400-79818400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:79810600-79815400	Weak transcription	Right Atrium	heart
18	chr7:79810800-79815400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr7:79811000-79816000	Weak transcription	Gastric	stomach
20	chr7:79811000-79817200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr7:79811600-79845000	Weak transcription	Primary T cells from cord blood	blood
22	chr7:79812000-79815200	Enhancers	H9 Cell Line	embryonic stem cell
23	chr7:79812000-79815200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr7:79812000-79816000	Enhancers	Fetal Lung	lung
25	chr7:79812400-79815000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr7:79812400-79815000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr7:79812400-79815400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr7:79812400-79815600	Weak transcription	A549	lung
29	chr7:79812400-79816000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:79812400-79816000	Weak transcription	NHDF-Ad	bronchial
31	chr7:79812400-79816000	Weak transcription	NHLF	lung
32	chr7:79812400-79818200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:79812400-79827800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:79812400-79827800	Weak transcription	NHEK	skin
35	chr7:79812400-79828200	Weak transcription	HMEC	breast
36	chr7:79812600-79815400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr7:79812800-79815400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr7:79812800-79817200	Enhancers	Adipose Nuclei	Adipose
39	chr7:79812800-79817600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr7:79813000-79815200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:79813000-79815400	Enhancers	Brain Hippocampus Middle	brain
42	chr7:79813000-79816000	Enhancers	Brain Angular Gyrus	brain
43	chr7:79813200-79818800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:79813400-79816000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:79813400-79816000	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:79813400-79816000	Weak transcription	Fetal Stomach	stomach
47	chr7:79813400-79829000	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:79813800-79816800	Enhancers	Brain Anterior Caudate	brain
49	chr7:79813800-79828000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr7:79814200-79815400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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