Variant report

Variant	rs9400038
Chromosome Location	chr6:107090369-107090370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11153020	0.92[CEU][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12199993	0.93[YRI][hapmap];0.97[AFR][1000 genomes]
rs1419055	0.81[CEU][hapmap]
rs1811546	0.83[CEU][hapmap]
rs2015205	0.85[CEU][hapmap]
rs2306098	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2353036	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3104039	0.81[CEU][hapmap]
rs3121447	0.86[AFR][1000 genomes]
rs3804345	0.82[CEU][hapmap]
rs6568448	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs6930885	0.82[CEU][hapmap]
rs727104	0.97[AFR][1000 genomes]
rs7750365	0.84[AFR][1000 genomes]
rs9373886	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9384626	0.83[CEU][hapmap]
rs9400035	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9400039	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9400040	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9400041	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9486434	0.82[CEU][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9400038	QRSL1	Cis_1M	lymphoblastoid	RTeQTL
rs9400038	QRSL1	cis	Nerve Tibial	GTEx
rs9400038	QRSL1	cis	Thyroid	GTEx
rs9400038	QRSL1	cis	normal skin	skin_eQTL
rs9400038	QRSL1	cis	Muscle Skeletal	GTEx
rs9400038	QRSL1	cis	Skin Sun Exposed Lower leg	GTEx
rs9400038	QRSL1	cis	multi-tissue	Pritchard
rs9400038	QRSL1	cis	Lymphoblastoid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:107078400-107090400	Weak transcription	HSMMtube	muscle
2	chr6:107078600-107090400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:107078600-107090400	Weak transcription	Esophagus	oesophagus
4	chr6:107078600-107090400	Weak transcription	Gastric	stomach
5	chr6:107078600-107090400	Weak transcription	HSMM	muscle
6	chr6:107078600-107090600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:107078600-107090600	Weak transcription	Fetal Brain Female	brain
8	chr6:107078600-107092000	Weak transcription	Brain Germinal Matrix	brain
9	chr6:107078600-107092600	Weak transcription	Brain Anterior Caudate	brain
10	chr6:107078600-107093000	Weak transcription	Colonic Mucosa	Colon
11	chr6:107078600-107100200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:107078600-107100400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:107078600-107103800	Weak transcription	Fetal Brain Male	brain
14	chr6:107078600-107104200	Weak transcription	Brain Angular Gyrus	brain
15	chr6:107078600-107106200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:107078600-107106600	Weak transcription	NH-A	brain
17	chr6:107078600-107110200	Weak transcription	NHLF	lung
18	chr6:107078600-107110800	Weak transcription	Fetal Heart	heart
19	chr6:107078600-107115200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:107078600-107125200	Weak transcription	Stomach Mucosa	stomach
21	chr6:107078800-107090400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:107078800-107090600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:107078800-107090600	Weak transcription	Hela-S3	cervix
24	chr6:107078800-107092000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:107078800-107093600	Weak transcription	NHEK	skin
26	chr6:107079400-107091000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:107079400-107092600	Weak transcription	HMEC	breast
28	chr6:107079400-107092800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:107079600-107090600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:107079600-107090800	Weak transcription	Osteobl	bone
31	chr6:107079600-107092400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:107081000-107092800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:107082600-107091800	Weak transcription	Lung	lung
34	chr6:107085000-107091200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:107085000-107112800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:107085200-107090400	Weak transcription	Fetal Kidney	kidney
37	chr6:107085400-107090400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:107085400-107090400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:107085400-107090800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:107085400-107100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:107085400-107114000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:107086000-107090400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:107086000-107094200	Strong transcription	Primary T cells from cord blood	blood
44	chr6:107086400-107104400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:107086600-107092600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:107086600-107094400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:107086600-107098200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:107086800-107091200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:107086800-107091200	Weak transcription	Psoas Muscle	Psoas
50	chr6:107087200-107090400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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