Variant report

Variant	rs9364106
Chromosome Location	chr6:71507158-71507159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1024211	0.82[JPT][hapmap]
rs10498874	0.82[JPT][hapmap]
rs10498875	0.82[JPT][hapmap]
rs10498876	0.82[JPT][hapmap]
rs10755541	0.82[JPT][hapmap]
rs10755543	0.82[JPT][hapmap]
rs10806636	0.81[JPT][hapmap]
rs1084388	0.82[JPT][hapmap]
rs10945243	0.82[JPT][hapmap]
rs10945246	0.82[JPT][hapmap]
rs10945247	0.82[JPT][hapmap]
rs10945262	0.82[JPT][hapmap]
rs12197239	0.81[JPT][hapmap]
rs12202843	0.82[JPT][hapmap]
rs12207501	0.82[JPT][hapmap]
rs12209357	0.82[JPT][hapmap]
rs12209431	0.82[JPT][hapmap]
rs12212629	0.82[JPT][hapmap]
rs12215757	0.82[JPT][hapmap]
rs12215915	0.93[YRI][hapmap]
rs1333964	0.82[JPT][hapmap]
rs1333967	0.82[JPT][hapmap]
rs1333968	0.92[CHD][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs1577110	0.82[JPT][hapmap]
rs2273566	0.88[LWK][hapmap];0.93[YRI][hapmap]
rs2347432	0.82[JPT][hapmap]
rs2347433	0.82[JPT][hapmap]
rs2474913	0.82[JPT][hapmap]
rs4282370	0.87[JPT][hapmap];0.86[YRI][hapmap]
rs4395687	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4410690	0.95[ASN][1000 genomes]
rs4580826	0.82[JPT][hapmap]
rs4613778	0.82[JPT][hapmap];0.86[YRI][hapmap]
rs4706460	0.88[LWK][hapmap];0.93[YRI][hapmap]
rs4706461	0.82[JPT][hapmap]
rs4706462	0.82[JPT][hapmap];0.80[LWK][hapmap];0.93[YRI][hapmap]
rs4706463	0.82[JPT][hapmap]
rs4706464	0.82[JPT][hapmap]
rs4707844	0.85[LWK][hapmap]
rs4707847	0.82[JPT][hapmap]
rs4707851	0.82[JPT][hapmap]
rs4707855	0.82[JPT][hapmap]
rs4707856	0.82[JPT][hapmap]
rs68097508	0.81[EUR][1000 genomes]
rs6919104	0.85[AFR][1000 genomes]
rs6927575	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[YRI][hapmap];0.99[ASN][1000 genomes]
rs6941789	0.82[AFR][1000 genomes]
rs7747310	0.92[YRI][hapmap]
rs7748778	0.93[YRI][hapmap]
rs7754217	0.88[LWK][hapmap];0.93[YRI][hapmap]
rs7760267	0.82[JPT][hapmap]
rs7771674	0.87[JPT][hapmap]
rs781963	0.82[JPT][hapmap]
rs781964	0.82[JPT][hapmap]
rs781967	0.82[JPT][hapmap]
rs781968	0.82[JPT][hapmap]
rs781969	0.82[JPT][hapmap];0.86[YRI][hapmap]
rs781971	0.93[JPT][hapmap]
rs781978	0.82[JPT][hapmap]
rs781982	0.82[JPT][hapmap]
rs781983	0.82[JPT][hapmap]
rs781985	0.82[JPT][hapmap]
rs781987	0.82[JPT][hapmap]
rs781989	0.82[JPT][hapmap]
rs781990	0.82[JPT][hapmap]
rs781992	0.82[JPT][hapmap]
rs9342795	0.85[YRI][hapmap]
rs9342796	0.83[ASW][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap]
rs9360426	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs9455215	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9364106	OGFRL1	cis	cerebellum	SCAN
rs9364106	MTO1	cis	cerebellum	SCAN
rs9364106	B3GAT2	cis	cerebellum	SCAN
rs9364106	SMAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71444800-71523600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr6:71466400-71508800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:71468800-71532200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:71473000-71515600	Weak transcription	Left Ventricle	heart
5	chr6:71473800-71520200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:71474600-71568800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:71474800-71515000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:71475000-71515200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:71481800-71515000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:71482200-71515600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:71483000-71515200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:71487600-71515600	Weak transcription	Thymus	Thymus
13	chr6:71489000-71517400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:71489000-71521800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:71489200-71517800	Weak transcription	Fetal Thymus	thymus
16	chr6:71489400-71515000	Weak transcription	Liver	Liver
17	chr6:71489600-71515600	Weak transcription	Primary T cells from cord blood	blood
18	chr6:71490400-71515600	Weak transcription	Pancreas	Pancrea
19	chr6:71491800-71526200	Weak transcription	HSMM	muscle
20	chr6:71492000-71522200	Weak transcription	Brain Angular Gyrus	brain
21	chr6:71492400-71508800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:71492400-71563600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:71492800-71515600	Weak transcription	Aorta	Aorta
24	chr6:71493000-71515600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:71493000-71526000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:71500200-71515600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:71500800-71514600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:71500800-71517600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:71501000-71515600	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:71501800-71520000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:71502400-71508600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:71503600-71522800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:71504200-71517000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:71504400-71515600	Weak transcription	Primary B cells from cord blood	blood
35	chr6:71504400-71515600	Weak transcription	Fetal Intestine Small	intestine
36	chr6:71504400-71517400	Weak transcription	Brain Anterior Caudate	brain
37	chr6:71505600-71534400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:71505800-71515600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:71506000-71515600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:71506200-71507600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:71506800-71570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:71507000-71507200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:71507000-71507600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr6:71507000-71507800	Enhancers	GM12878-XiMat	blood

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