Variant report

Variant	rs11028
Chromosome Location	chr7:66276217-66276218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10234018	0.82[YRI][hapmap]
rs10252765	0.87[ASW][hapmap]
rs10263935	0.82[YRI][hapmap]
rs10267335	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10281796	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12530806	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12536410	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12698546	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698547	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13220977	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13227468	0.83[EUR][1000 genomes]
rs13231140	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13241598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2244022	0.82[YRI][hapmap]
rs2707853	0.82[YRI][hapmap]
rs2707854	0.93[ASW][hapmap];0.80[LWK][hapmap]
rs2707856	0.93[ASW][hapmap];0.80[LWK][hapmap]
rs28441684	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28648401	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2901311	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs34577323	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3764903	0.93[ASW][hapmap];0.82[YRI][hapmap]
rs3800817	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800820	0.85[YRI][hapmap]
rs4717328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4717331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718412	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718422	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4718424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718428	0.93[ASW][hapmap];0.82[LWK][hapmap]
rs4718430	0.83[EUR][1000 genomes]
rs6460308	0.82[YRI][hapmap]
rs68168107	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6958520	0.93[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11028	GUSB	cis	parietal	SCAN
rs11028	RP4-756H11.3	cis	lung	GTEx
rs11028	CRCP	cis	parietal	SCAN
rs11028	CRCP	cis	cerebellum	SCAN
rs11028	RP4-756H11.3	cis	Thyroid	GTEx
rs11028	GUSB	cis	cerebellum	SCAN
rs11028	RP4-756H11.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:66236800-66276800	Strong transcription	Dnd41	blood
3	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:66238200-66276600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr7:66245600-66279200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:66245600-66279400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:66246200-66277800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:66246200-66279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:66248400-66277800	Strong transcription	Osteobl	bone
12	chr7:66248600-66276800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:66248800-66277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:66249400-66278600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:66250000-66279200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:66250000-66279200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:66250200-66277800	Strong transcription	Primary T cells from cord blood	blood
18	chr7:66250200-66278600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr7:66253200-66277600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:66254000-66277400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:66254000-66278400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:66254200-66277200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr7:66254200-66278600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:66254600-66278600	Strong transcription	HSMM	muscle
25	chr7:66254800-66276800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr7:66254800-66276800	Strong transcription	HepG2	liver
27	chr7:66254800-66277800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr7:66255200-66277000	Strong transcription	HMEC	breast
29	chr7:66255600-66277200	Weak transcription	Fetal Heart	heart
30	chr7:66255600-66279800	Weak transcription	Right Atrium	heart
31	chr7:66256200-66278600	Strong transcription	Adipose Nuclei	Adipose
32	chr7:66256600-66278400	Strong transcription	Fetal Muscle Leg	muscle
33	chr7:66256600-66278600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:66256600-66279000	Strong transcription	Fetal Stomach	stomach
35	chr7:66257000-66276800	Strong transcription	Fetal Intestine Large	intestine
36	chr7:66257200-66277800	Strong transcription	Ovary	ovary
37	chr7:66257200-66278400	Strong transcription	Thymus	Thymus
38	chr7:66257600-66278600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:66258400-66277000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr7:66258600-66277000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:66258600-66277200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:66259200-66276600	Strong transcription	Fetal Brain Female	brain
43	chr7:66259400-66276800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:66259400-66276800	Strong transcription	Fetal Thymus	thymus
45	chr7:66259400-66277000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:66259600-66277600	Strong transcription	Placenta	Placenta
47	chr7:66259800-66276800	Strong transcription	Liver	Liver
48	chr7:66259800-66277000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:66259800-66277200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:66259800-66277800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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