Variant report

Variant	rs9400035
Chromosome Location	chr6:107090122-107090123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11153020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12199993	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1419055	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2306098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3121447	0.86[AFR][1000 genomes]
rs727104	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7750365	0.84[AFR][1000 genomes]
rs9373886	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9400038	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9400039	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv970157	chr6:107089574-107090964	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9400035	QRSL1	cis	Thyroid	GTEx
rs9400035	QRSL1	cis	Muscle Skeletal	GTEx
rs9400035	QRSL1	cis	lung	GTEx
rs9400035	QRSL1	cis	Skin Sun Exposed Lower leg	GTEx
rs9400035	QRSL1	Cis_1M	lymphoblastoid	RTeQTL
rs9400035	QRSL1	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:107078400-107090400	Weak transcription	HSMMtube	muscle
2	chr6:107078600-107090200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:107078600-107090200	Weak transcription	Fetal Intestine Large	intestine
4	chr6:107078600-107090200	Weak transcription	Fetal Lung	lung
5	chr6:107078600-107090200	Weak transcription	Ovary	ovary
6	chr6:107078600-107090400	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:107078600-107090400	Weak transcription	Esophagus	oesophagus
8	chr6:107078600-107090400	Weak transcription	Gastric	stomach
9	chr6:107078600-107090400	Weak transcription	HSMM	muscle
10	chr6:107078600-107090600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:107078600-107090600	Weak transcription	Fetal Brain Female	brain
12	chr6:107078600-107092000	Weak transcription	Brain Germinal Matrix	brain
13	chr6:107078600-107092600	Weak transcription	Brain Anterior Caudate	brain
14	chr6:107078600-107093000	Weak transcription	Colonic Mucosa	Colon
15	chr6:107078600-107100200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:107078600-107100400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:107078600-107103800	Weak transcription	Fetal Brain Male	brain
18	chr6:107078600-107104200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:107078600-107106200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:107078600-107106600	Weak transcription	NH-A	brain
21	chr6:107078600-107110200	Weak transcription	NHLF	lung
22	chr6:107078600-107110800	Weak transcription	Fetal Heart	heart
23	chr6:107078600-107115200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:107078600-107125200	Weak transcription	Stomach Mucosa	stomach
25	chr6:107078800-107090200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:107078800-107090400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:107078800-107090600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:107078800-107090600	Weak transcription	Hela-S3	cervix
29	chr6:107078800-107092000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:107078800-107093600	Weak transcription	NHEK	skin
31	chr6:107079400-107091000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:107079400-107092600	Weak transcription	HMEC	breast
33	chr6:107079400-107092800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:107079600-107090600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:107079600-107090800	Weak transcription	Osteobl	bone
36	chr6:107079600-107092400	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:107081000-107092800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:107082600-107091800	Weak transcription	Lung	lung
39	chr6:107085000-107091200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:107085000-107112800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:107085200-107090200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:107085200-107090400	Weak transcription	Fetal Kidney	kidney
43	chr6:107085400-107090200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:107085400-107090200	Weak transcription	Adipose Nuclei	Adipose
45	chr6:107085400-107090200	Weak transcription	Thymus	Thymus
46	chr6:107085400-107090400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:107085400-107090400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:107085400-107090800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:107085400-107100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:107085400-107114000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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