Variant report

Variant	rs9648369
Chromosome Location	chr7:30608662-30608663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10227133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10232372	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10237725	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs10239660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10243040	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10249885	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10265589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10480088	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1074373	0.96[ASN][1000 genomes]
rs10951271	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1141114	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13228758	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1468402	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1558064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16875282	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16875285	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2009662	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2214837	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267710	0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2270025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2391870	0.80[EUR][1000 genomes]
rs3779250	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3807632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4722992	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4722999	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6462211	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6947982	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6970688	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6970807	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9648369	AC005154.6	cis	Artery Tibial	GTEx
rs9648369	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs9648369	AC005154.6	cis	Nerve Tibial	GTEx
rs9648369	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs9648369	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs9648369	AC005154.6	cis	Thyroid	GTEx
rs9648369	AC005154.6	cis	Whole Blood	GTEx
rs9648369	AC005154.6	cis	lung	GTEx
rs9648369	AC005154.6	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
2	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
3	chr7:30591200-30610200	Weak transcription	Small Intestine	intestine
4	chr7:30591200-30612400	Weak transcription	Brain Germinal Matrix	brain
5	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
6	chr7:30593800-30609400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:30595600-30609000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr7:30595800-30608800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:30596600-30614400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:30597600-30624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:30598400-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr7:30599400-30610000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:30599400-30617400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:30601800-30612000	Weak transcription	Aorta	Aorta
16	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
17	chr7:30602800-30615400	Weak transcription	Fetal Brain Female	brain
18	chr7:30602800-30616200	Weak transcription	Fetal Brain Male	brain
19	chr7:30603200-30621000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:30603600-30610200	Weak transcription	A549	lung
22	chr7:30603600-30612600	Weak transcription	Colonic Mucosa	Colon
23	chr7:30603800-30612200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:30604000-30609000	Strong transcription	Liver	Liver
25	chr7:30604000-30610600	Weak transcription	HMEC	breast
26	chr7:30604000-30612200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:30604000-30612400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:30604000-30612800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:30604000-30613000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:30604000-30613600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:30604000-30615000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:30604000-30615200	Weak transcription	HepG2	liver
33	chr7:30604000-30615200	Weak transcription	NHEK	skin
34	chr7:30604000-30615400	Weak transcription	NHDF-Ad	bronchial
35	chr7:30604200-30610200	Weak transcription	GM12878-XiMat	blood
36	chr7:30604200-30613400	Weak transcription	HUVEC	blood vessel
37	chr7:30604400-30610000	Weak transcription	Thymus	Thymus
38	chr7:30604400-30612000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:30604600-30617800	Weak transcription	Right Ventricle	heart
40	chr7:30604600-30624400	Weak transcription	Gastric	stomach
41	chr7:30605200-30609200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:30605200-30609400	Strong transcription	Primary B cells from cord blood	blood
43	chr7:30605400-30609200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:30605600-30608800	Strong transcription	Adipose Nuclei	Adipose
45	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:30606200-30611000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:30606400-30608800	Strong transcription	Fetal Intestine Large	intestine
48	chr7:30606400-30609000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr7:30606600-30608800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr7:30606600-30609200	Strong transcription	HSMMtube	muscle

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