Variant report

Variant	rs10247899
Chromosome Location	chr7:65233486-65233487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10250008	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10279930	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2272185	0.83[ASN][1000 genomes]
rs2419433	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2419434	0.85[EUR][1000 genomes]
rs2690405	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2900904	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3734912	0.85[ASN][1000 genomes]
rs4718267	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4718269	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4718270	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4718273	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4718274	0.81[AMR][1000 genomes]
rs4718276	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4718277	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6460260	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460261	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7781958	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7789975	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517778	chr7:64462326-65326821	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv917231	chr7:64478253-65300317	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1029796	chr7:64494934-65302696	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv3339156	chr7:64510176-65349050	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv2764020	chr7:64594065-65351820	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv1018447	chr7:64609892-65308719	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv538897	chr7:64609892-65308719	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv1029942	chr7:64679680-65371565	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv538903	chr7:64679680-65371565	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
13	nsv1019667	chr7:64679680-65380603	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
14	esv2757227	chr7:64694241-65373851	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
15	nsv1025207	chr7:65092426-65339879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
16	nsv1033400	chr7:65092426-65339879	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
17	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
18	nsv1020622	chr7:65161364-65339879	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10247899	GUSB	cis	Whole Blood	GTEx
rs10247899	VKORC1L1	cis	Whole Blood	GTEx
rs10247899	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10247899	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65216600-65235400	Weak transcription	Spleen	Spleen
2	chr7:65216800-65235200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:65216800-65235200	Weak transcription	Brain Hippocampus Middle	brain
4	chr7:65216800-65235200	Weak transcription	Left Ventricle	heart
5	chr7:65216800-65235200	Weak transcription	Lung	lung
6	chr7:65216800-65235200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:65217000-65235200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:65217200-65235200	Weak transcription	Psoas Muscle	Psoas
9	chr7:65217400-65235000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:65217400-65235000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:65217400-65235000	Weak transcription	Right Ventricle	heart
12	chr7:65217400-65235200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:65217400-65235200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:65217400-65235200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:65217400-65235200	Weak transcription	Primary B cells from cord blood	blood
16	chr7:65217400-65235200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr7:65217400-65235200	Weak transcription	Brain Anterior Caudate	brain
18	chr7:65217400-65235200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:65217400-65235200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:65217400-65235200	Weak transcription	Colonic Mucosa	Colon
21	chr7:65217400-65235200	Weak transcription	Esophagus	oesophagus
22	chr7:65217400-65235200	Weak transcription	Fetal Kidney	kidney
23	chr7:65217400-65235200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr7:65217400-65235200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:65217400-65235200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:65217400-65235400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:65217400-65235400	Weak transcription	Fetal Brain Male	brain
28	chr7:65217400-65235400	Weak transcription	Fetal Heart	heart
29	chr7:65217600-65235200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr7:65218000-65234200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr7:65218000-65235200	Weak transcription	Brain Angular Gyrus	brain
32	chr7:65218000-65235200	Weak transcription	Brain Substantia Nigra	brain
33	chr7:65218000-65235200	Weak transcription	Small Intestine	intestine
34	chr7:65218400-65235200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:65218600-65234800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr7:65219400-65235200	Weak transcription	Primary T cells from cord blood	blood
37	chr7:65219400-65235200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:65219400-65235400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr7:65219800-65235200	Weak transcription	NHLF	lung
40	chr7:65220000-65235200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:65220600-65234800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:65221000-65234800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:65221000-65235200	Weak transcription	GM12878-XiMat	blood
44	chr7:65221400-65235200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:65225800-65235200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:65226200-65235200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr7:65226200-65235200	Weak transcription	Brain Germinal Matrix	brain
48	chr7:65226200-65235200	Weak transcription	Colon Smooth Muscle	Colon
49	chr7:65226200-65235200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:65226200-65235400	Weak transcription	Fetal Lung	lung

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