Variant report

Variant	rs28682868
Chromosome Location	chr7:65689809-65689810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65685457..65687424-chr7:65688935..65691579,2	K562	blood:

Variant related genes	Relation type
ENSG00000169902	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1002053	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10215948	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10256544	0.81[EUR][1000 genomes]
rs10257427	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10267430	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11765965	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11971949	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11974219	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11974264	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13225383	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13309935	0.81[EUR][1000 genomes]
rs1540651	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1565531	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1643395	0.83[EUR][1000 genomes]
rs1695815	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1968225	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2036264	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2077593	0.81[EUR][1000 genomes]
rs2087647	0.81[AMR][1000 genomes]
rs2173570	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2420168	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35028832	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3935391	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4717292	0.82[EUR][1000 genomes]
rs4718328	0.83[AMR][1000 genomes]
rs4718330	0.83[AMR][1000 genomes]
rs4718343	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4718344	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55748098	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55962648	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6460291	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6460292	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6460295	0.82[EUR][1000 genomes]
rs6460296	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6945843	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6946143	0.81[AMR][1000 genomes]
rs6956179	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6958484	0.81[AMR][1000 genomes]
rs6960476	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6961990	0.81[EUR][1000 genomes]
rs6963646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971509	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6974614	0.81[AMR][1000 genomes]
rs6977501	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6979382	0.80[EUR][1000 genomes]
rs709595	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs709597	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7783613	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs778682	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs778685	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs778689	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs778692	0.81[EUR][1000 genomes]
rs778694	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778695	0.82[AMR][1000 genomes]
rs778699	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778700	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778706	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs778708	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs778709	0.82[EUR][1000 genomes]
rs778710	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs778712	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs778721	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs778723	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs778726	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs778727	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs778735	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7791891	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7794930	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7799834	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7801282	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7803424	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs875971	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs937495	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9969301	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9986696	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs28682868	GS1-124K5.4	cis	Whole Blood	GTEx
rs28682868	GTF2IRD1P1	cis	Thyroid	GTEx
rs28682868	GS1-124K5.11	cis	Thyroid	GTEx
rs28682868	GS1-124K5.4	cis	Stomach	GTEx
rs28682868	RP4-756H11.3	cis	Artery Aorta	GTEx
rs28682868	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs28682868	RNU6-96P	cis	Thyroid	GTEx
rs28682868	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs28682868	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs28682868	RP4-756H11.3	cis	Artery Tibial	GTEx
rs28682868	RP4-756H11.3	cis	Thyroid	GTEx
rs28682868	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs28682868	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs28682868	GS1-124K5.4	cis	Artery Aorta	GTEx
rs28682868	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28682868	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs28682868	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs28682868	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
2	chr7:65676000-65696200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:65676000-65716800	Weak transcription	Primary B cells from cord blood	blood
4	chr7:65676200-65696200	Weak transcription	Fetal Stomach	stomach
5	chr7:65676600-65691200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:65676600-65693200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:65677000-65694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:65677200-65693800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:65684200-65690000	Enhancers	Liver	Liver
10	chr7:65685600-65696200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:65686800-65701600	Weak transcription	Osteobl	bone
12	chr7:65686800-65715400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:65687000-65701800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:65687000-65701800	Weak transcription	NHDF-Ad	bronchial
15	chr7:65687800-65701800	Weak transcription	Spleen	Spleen
16	chr7:65687800-65703400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:65688600-65690000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:65688800-65690200	Enhancers	Ovary	ovary
19	chr7:65689400-65703600	Weak transcription	NHLF	lung
20	chr7:65689600-65691200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:65689600-65695800	Weak transcription	Brain Substantia Nigra	brain
22	chr7:65689600-65696200	Weak transcription	Lung	lung
23	chr7:65689600-65697800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:65689600-65701800	Weak transcription	Gastric	stomach
25	chr7:65689600-65715800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:65689800-65695000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:65689800-65695600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:65689800-65696200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:65689800-65697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:65689800-65701800	Weak transcription	Fetal Lung	lung
31	chr7:65689800-65701800	Weak transcription	HMEC	breast
32	chr7:65689800-65702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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