Variant report

Variant	rs769217
Chromosome Location	chr11:34482908-34482909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10836244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032700	0.81[MKK][hapmap]
rs1408034	0.87[LWK][hapmap]
rs1408035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408036	0.87[LWK][hapmap]
rs2076556	0.96[GIH][hapmap]
rs208681	0.85[GIH][hapmap]
rs208682	0.85[GIH][hapmap]
rs208683	0.85[GIH][hapmap]
rs2284365	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2284367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284368	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284369	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300182	0.92[GIH][hapmap]
rs2420388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758733	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3781711	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4755372	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755373	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756153	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs480575	0.83[TSI][hapmap]
rs482322	0.83[TSI][hapmap]
rs484214	0.83[TSI][hapmap]
rs524154	0.83[TSI][hapmap]
rs525938	0.83[TSI][hapmap]
rs554576	0.83[ASN][1000 genomes]
rs566979	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs6484722	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102889	0.88[GIH][hapmap]
rs7113917	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769218	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928213	0.89[ASN][1000 genomes]
rs942222	0.88[GIH][hapmap]
rs942223	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs769217	CAT	cis	cerebellum	SCAN
rs769217	CAT	cis	Whole Blood	GTEx
rs769217	CAT	cis	lymphoblastoid	seeQTL
rs769217	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs769217	CAT	cis	Artery Tibial	GTEx
rs769217	CAT	cis	parietal	SCAN
rs769217	TRAF6	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34461800-34485800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:34469800-34487400	Strong transcription	Hela-S3	cervix
3	chr11:34470200-34486600	Genic enhancers	Liver	Liver
4	chr11:34470400-34487400	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:34470800-34488000	Strong transcription	Brain Hippocampus Middle	brain
6	chr11:34470800-34488000	Strong transcription	Fetal Intestine Large	intestine
7	chr11:34470800-34494200	Strong transcription	Brain Germinal Matrix	brain
8	chr11:34470800-34495600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr11:34471000-34485400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:34471000-34487200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr11:34471000-34487400	Strong transcription	Osteobl	bone
12	chr11:34471000-34494000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr11:34471200-34483400	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr11:34471200-34487000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:34471400-34486400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:34471400-34486600	Strong transcription	Primary T cells from cord blood	blood
17	chr11:34471400-34487000	Strong transcription	Thymus	Thymus
18	chr11:34471400-34487200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:34471400-34487200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr11:34471400-34487400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:34471400-34487400	Strong transcription	Ovary	ovary
22	chr11:34471400-34487400	Strong transcription	Dnd41	blood
23	chr11:34471400-34487400	Strong transcription	HSMM	muscle
24	chr11:34471400-34487600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:34471400-34487800	Strong transcription	Colon Smooth Muscle	Colon
26	chr11:34471400-34488000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:34471400-34488000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:34471400-34494000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:34471400-34494600	Strong transcription	Placenta	Placenta
30	chr11:34471400-34495000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:34471400-34496400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:34471600-34484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:34471600-34487200	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:34471600-34487800	Strong transcription	HSMMtube	muscle
35	chr11:34471600-34488000	Strong transcription	Fetal Thymus	thymus
36	chr11:34471600-34495200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr11:34471600-34496800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr11:34472600-34485200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:34473200-34485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:34473200-34487200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:34473600-34485200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:34473600-34488000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:34473800-34485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:34473800-34486400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr11:34474000-34485800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr11:34474000-34487800	Strong transcription	Lung	lung
47	chr11:34474000-34496800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr11:34474200-34485000	Strong transcription	Primary B cells from cord blood	blood
49	chr11:34474800-34487200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:34475400-34483600	Strong transcription	Aorta	Aorta

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