Variant report

Variant	rs10480088
Chromosome Location	chr7:30619996-30619997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:30615137..30618077-chr7:30619894..30622541,2	K562	blood:
2	chr7:30619854..30624580-chr7:30627749..30633605,6	K562	blood:

Variant related genes	Relation type
ENSG00000196295	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10227133	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10232372	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233132	0.81[ASN][1000 genomes]
rs10237725	0.85[EUR][1000 genomes]
rs10239660	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10243040	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249885	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265589	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074373	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951271	0.83[ASN][1000 genomes]
rs1141114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761080	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532057	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533961	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228758	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468402	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875282	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009662	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214837	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240401	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267710	0.84[ASN][1000 genomes]
rs2270025	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391870	0.81[EUR][1000 genomes]
rs3779250	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807632	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722992	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722999	0.86[ASN][1000 genomes]
rs6462211	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947982	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6970688	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970807	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9648369	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024458	chr7:30601877-30649659	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10480088	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs10480088	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs10480088	AC005154.6	cis	Nerve Tibial	GTEx
rs10480088	AC005154.6	cis	lung	GTEx
rs10480088	AC005154.6	cis	Artery Tibial	GTEx
rs10480088	AC005154.6	cis	Thyroid	GTEx
rs10480088	AC005154.6	cis	Esophagus Mucosa	GTEx
rs10480088	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
2	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
3	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:30597600-30624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:30598400-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
7	chr7:30603200-30621000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:30604600-30624400	Weak transcription	Gastric	stomach
10	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:30607000-30633400	Weak transcription	Fetal Kidney	kidney
12	chr7:30609800-30621400	Weak transcription	K562	blood
13	chr7:30612200-30625000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:30612200-30625600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:30612200-30627000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:30612800-30628600	Weak transcription	Stomach Mucosa	stomach
17	chr7:30614000-30620200	Weak transcription	Aorta	Aorta
18	chr7:30614000-30623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr7:30614000-30633200	Weak transcription	HUVEC	blood vessel
20	chr7:30615600-30633200	Weak transcription	Brain Germinal Matrix	brain
21	chr7:30615600-30633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:30615800-30627000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:30616000-30622000	Strong transcription	A549	lung
24	chr7:30616000-30625400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:30616200-30620800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:30616200-30620800	Strong transcription	Ovary	ovary
27	chr7:30616200-30621200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:30616200-30627800	Strong transcription	Primary T cells from cord blood	blood
29	chr7:30616400-30625000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr7:30616600-30625000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:30616600-30625400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr7:30616800-30625600	Strong transcription	Liver	Liver
33	chr7:30617000-30622600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr7:30617200-30620600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:30617200-30621200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:30617200-30621400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:30617200-30621600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr7:30617200-30624800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:30617200-30625800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:30617200-30626000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:30617200-30626000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:30617200-30627200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr7:30617400-30620800	Strong transcription	Brain Angular Gyrus	brain
44	chr7:30617400-30621000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:30617400-30621200	Strong transcription	Fetal Stomach	stomach
46	chr7:30617400-30621400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:30617400-30625600	Strong transcription	Fetal Intestine Large	intestine
48	chr7:30617400-30626000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:30617600-30621600	Strong transcription	Brain Anterior Caudate	brain
50	chr7:30617600-30622200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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