Variant report

Variant	rs7109778
Chromosome Location	chr11:34482189-34482190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1033509	0.88[ASN][1000 genomes]
rs10488737	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10742316	0.88[ASN][1000 genomes]
rs12421999	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16925614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16925662	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16925668	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16925673	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16925678	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2076556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs208675	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs208677	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs208680	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs208681	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs208682	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs208683	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2231819	0.81[EUR][1000 genomes]
rs2300182	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746169	0.88[ASN][1000 genomes]
rs3758735	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3758736	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3758737	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3758738	0.82[EUR][1000 genomes]
rs4755374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756146	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4756151	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4756155	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4756156	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs489554	0.95[ASN][1000 genomes]
rs5026711	0.88[ASN][1000 genomes]
rs55633825	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55665450	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55941777	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56291727	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs564250	0.97[ASN][1000 genomes]
rs7102889	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7104121	0.82[EUR][1000 genomes]
rs7104394	0.82[EUR][1000 genomes]
rs7106485	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7109462	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7115064	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7126085	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7126243	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7130331	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7130345	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72923163	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72924903	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72924928	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72927347	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72927368	0.82[EUR][1000 genomes]
rs72927369	0.82[EUR][1000 genomes]
rs7395059	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7928866	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7935626	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7938373	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7109778	CAT	cis	Whole Blood	GTEx
rs7109778	CAT	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34461400-34482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:34461800-34485800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:34469800-34487400	Strong transcription	Hela-S3	cervix
4	chr11:34470200-34486600	Genic enhancers	Liver	Liver
5	chr11:34470400-34482800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:34470400-34487400	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:34470800-34488000	Strong transcription	Brain Hippocampus Middle	brain
8	chr11:34470800-34488000	Strong transcription	Fetal Intestine Large	intestine
9	chr11:34470800-34494200	Strong transcription	Brain Germinal Matrix	brain
10	chr11:34470800-34495600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr11:34471000-34485400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:34471000-34487200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr11:34471000-34487400	Strong transcription	Osteobl	bone
14	chr11:34471000-34494000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr11:34471200-34483400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:34471200-34487000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:34471400-34486400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:34471400-34486600	Strong transcription	Primary T cells from cord blood	blood
19	chr11:34471400-34487000	Strong transcription	Thymus	Thymus
20	chr11:34471400-34487200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:34471400-34487200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:34471400-34487400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:34471400-34487400	Strong transcription	Ovary	ovary
24	chr11:34471400-34487400	Strong transcription	Dnd41	blood
25	chr11:34471400-34487400	Strong transcription	HSMM	muscle
26	chr11:34471400-34487600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:34471400-34487800	Strong transcription	Colon Smooth Muscle	Colon
28	chr11:34471400-34488000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr11:34471400-34488000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:34471400-34494000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:34471400-34494600	Strong transcription	Placenta	Placenta
32	chr11:34471400-34495000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:34471400-34496400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:34471600-34484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:34471600-34487200	Strong transcription	Fetal Muscle Leg	muscle
36	chr11:34471600-34487800	Strong transcription	HSMMtube	muscle
37	chr11:34471600-34488000	Strong transcription	Fetal Thymus	thymus
38	chr11:34471600-34495200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr11:34471600-34496800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr11:34472600-34482800	Weak transcription	Right Atrium	heart
41	chr11:34472600-34485200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:34472800-34482600	Weak transcription	Brain Angular Gyrus	brain
43	chr11:34473200-34485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:34473200-34487200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:34473600-34485200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:34473600-34488000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:34473800-34485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:34473800-34486400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr11:34474000-34485800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr11:34474000-34487800	Strong transcription	Lung	lung

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