Variant report

Variant	rs3740994
Chromosome Location	chr11:5699801-5699802
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10769173	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838517	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2342390	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2880345	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3740995	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3740996	0.87[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4347418	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7929587	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3740994	OR52E6	cis	parietal	SCAN
rs3740994	TRIM6-TRIM34	cis	cerebellum	SCAN
rs3740994	OR51V1	cis	parietal	SCAN
rs3740994	C11orf21	cis	cerebellum	SCAN
rs3740994	PGAP2	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5674800-5705400	Weak transcription	Psoas Muscle	Psoas
2	chr11:5684000-5700000	Weak transcription	Right Ventricle	heart
3	chr11:5684000-5705400	Weak transcription	Brain Substantia Nigra	brain
4	chr11:5684200-5705400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr11:5684600-5703600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:5685400-5705400	Weak transcription	Stomach Mucosa	stomach
7	chr11:5688000-5705600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:5691000-5705000	Weak transcription	Hela-S3	cervix
9	chr11:5691000-5705400	Weak transcription	Fetal Brain Male	brain
10	chr11:5694200-5705400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:5696000-5705200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:5697000-5705600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr11:5698200-5705400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:5698600-5702400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:5698800-5700200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr11:5698800-5700400	Strong transcription	Colonic Mucosa	Colon
17	chr11:5698800-5700600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:5698800-5700800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:5698800-5701200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr11:5698800-5701200	Strong transcription	Colon Smooth Muscle	Colon
21	chr11:5698800-5701400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:5698800-5701400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:5698800-5701400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:5698800-5701400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:5698800-5701400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:5698800-5701400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:5698800-5701400	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr11:5698800-5701400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:5698800-5701400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:5698800-5701400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:5698800-5701400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:5698800-5701400	Strong transcription	Fetal Intestine Large	intestine
33	chr11:5698800-5701400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr11:5698800-5701400	Strong transcription	Fetal Muscle Leg	muscle
35	chr11:5698800-5701400	Strong transcription	Lung	lung
36	chr11:5698800-5701400	Strong transcription	Ovary	ovary
37	chr11:5698800-5701400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:5698800-5701400	Strong transcription	Thymus	Thymus
39	chr11:5698800-5701400	Strong transcription	Osteobl	bone
40	chr11:5698800-5701600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:5698800-5701600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:5698800-5701600	Strong transcription	Liver	Liver
43	chr11:5698800-5701600	Strong transcription	Placenta	Placenta
44	chr11:5698800-5701600	Strong transcription	Fetal Stomach	stomach
45	chr11:5698800-5701600	Strong transcription	Fetal Thymus	thymus
46	chr11:5698800-5701800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:5698800-5701800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr11:5698800-5701800	Strong transcription	HSMMtube	muscle
49	chr11:5698800-5702000	Strong transcription	Dnd41	blood
50	chr11:5698800-5702200	Strong transcription	Primary monocytes fromperipheralblood	blood

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