Variant report

Variant	rs9400040
Chromosome Location	chr6:107091199-107091200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs11153020	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12199993	0.94[ASW][hapmap];0.81[CEU][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1419055	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1811546	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs2015205	0.88[CEU][hapmap];0.93[GIH][hapmap]
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]
rs3104039	0.84[CEU][hapmap]
rs3121447	0.86[AFR][1000 genomes]
rs3804345	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs6930885	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs727104	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7750365	0.83[ASW][hapmap];0.84[AFR][1000 genomes]
rs898896	0.81[JPT][hapmap]
rs9373886	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9384626	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs9400035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400038	0.96[CEU][hapmap];1.00[YRI][hapmap];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]
rs9400041	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486434	0.85[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9400040	QRSL1	cis	Muscle Skeletal	GTEx
rs9400040	QRSL1	Cis_1M	lymphoblastoid	RTeQTL
rs9400040	QRSL1	cis	parietal	SCAN
rs9400040	QRSL1	cis	lung	GTEx
rs9400040	QRSL1	cis	cerebellum	SCAN
rs9400040	QRSL1	cis	Lymphoblastoid	GTEx
rs9400040	QRSL1	cis	Skin Sun Exposed Lower leg	GTEx
rs9400040	QRSL1	cis	Nerve Tibial	GTEx
rs9400040	QRSL1	cis	Thyroid	GTEx
rs9400040	QRSL1	cis	multi-tissue	Pritchard
rs9400040	QRSL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:107078600-107092000	Weak transcription	Brain Germinal Matrix	brain
2	chr6:107078600-107092600	Weak transcription	Brain Anterior Caudate	brain
3	chr6:107078600-107093000	Weak transcription	Colonic Mucosa	Colon
4	chr6:107078600-107100200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:107078600-107100400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:107078600-107103800	Weak transcription	Fetal Brain Male	brain
7	chr6:107078600-107104200	Weak transcription	Brain Angular Gyrus	brain
8	chr6:107078600-107106200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:107078600-107106600	Weak transcription	NH-A	brain
10	chr6:107078600-107110200	Weak transcription	NHLF	lung
11	chr6:107078600-107110800	Weak transcription	Fetal Heart	heart
12	chr6:107078600-107115200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:107078600-107125200	Weak transcription	Stomach Mucosa	stomach
14	chr6:107078800-107092000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:107078800-107093600	Weak transcription	NHEK	skin
16	chr6:107079400-107092600	Weak transcription	HMEC	breast
17	chr6:107079400-107092800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:107079600-107092400	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:107081000-107092800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:107082600-107091800	Weak transcription	Lung	lung
21	chr6:107085000-107091200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:107085000-107112800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:107085400-107100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:107085400-107114000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:107086000-107094200	Strong transcription	Primary T cells from cord blood	blood
26	chr6:107086400-107104400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:107086600-107092600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:107086600-107094400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:107086600-107098200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:107086800-107091200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:107086800-107091200	Weak transcription	Psoas Muscle	Psoas
32	chr6:107087200-107112600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:107087400-107094200	Weak transcription	A549	lung
34	chr6:107087400-107106200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:107087600-107095600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:107087800-107094400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:107087800-107094400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr6:107087800-107094600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:107087800-107094600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr6:107087800-107094800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:107087800-107095400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:107087800-107104000	Strong transcription	Dnd41	blood
43	chr6:107088000-107092600	Strong transcription	Fetal Thymus	thymus
44	chr6:107088000-107094600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:107088000-107095400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:107088000-107104000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:107088000-107106000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:107088000-107108000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:107088200-107094600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:107088200-107095000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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