Variant report

Variant	rs1793336
Chromosome Location	chr11:77605501-77605502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10698394	0.84[EUR][1000 genomes]
rs10751278	0.82[ASN][1000 genomes]
rs10793262	0.89[EUR][1000 genomes]
rs10793263	0.81[ASN][1000 genomes]
rs10793264	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899402	0.84[EUR][1000 genomes]
rs10899403	0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs10899405	0.85[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs10899406	0.85[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs10899407	0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs10899408	0.85[CHB][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs10899409	0.85[CHB][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs11237284	0.89[EUR][1000 genomes]
rs11237289	0.89[EUR][1000 genomes]
rs11237295	0.85[CHB][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11237299	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11237303	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11518811	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12364072	0.89[EUR][1000 genomes]
rs1613945	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1783546	0.93[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790235	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790240	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790246	0.85[CHB][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs1790250	0.81[CHB][hapmap]
rs1793334	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793341	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793343	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs2212317	0.85[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2298819	0.82[EUR][1000 genomes]
rs2510967	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3018415	0.92[ASN][1000 genomes]
rs4245453	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945206	0.84[EUR][1000 genomes]
rs496786	0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs574665	0.82[EUR][1000 genomes]
rs61900164	0.89[EUR][1000 genomes]
rs7110670	0.80[CHB][hapmap]
rs7110924	0.84[EUR][1000 genomes]
rs7358471	0.89[EUR][1000 genomes]
rs7925343	0.89[EUR][1000 genomes]
rs7927913	0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7931272	0.85[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs7938133	0.80[CHB][hapmap]
rs9988883	0.85[CHB][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.85[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	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv555453	chr11:77577494-77618441	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv975954	chr11:77600915-77617903	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1793336	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
2	chr11:77579200-77625000	Weak transcription	HMEC	breast
3	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
5	chr11:77586600-77625000	Weak transcription	Stomach Mucosa	stomach
6	chr11:77587200-77617600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:77588200-77614000	Weak transcription	Right Ventricle	heart
8	chr11:77591200-77605600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
11	chr11:77593800-77625000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:77595400-77620000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:77597400-77617400	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:77597400-77625000	Weak transcription	A549	lung
16	chr11:77597600-77617400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:77597600-77629400	Weak transcription	Brain Germinal Matrix	brain
18	chr11:77597800-77605600	Weak transcription	Fetal Lung	lung
19	chr11:77597800-77609600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:77597800-77612200	Weak transcription	Brain Anterior Caudate	brain
21	chr11:77597800-77613600	Weak transcription	Fetal Intestine Large	intestine
22	chr11:77597800-77614000	Weak transcription	Lung	lung
23	chr11:77597800-77614000	Weak transcription	HSMMtube	muscle
24	chr11:77597800-77614200	Weak transcription	Brain Angular Gyrus	brain
25	chr11:77597800-77614200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:77597800-77614400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:77597800-77617400	Weak transcription	GM12878-XiMat	blood
28	chr11:77597800-77617600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:77597800-77617600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:77597800-77617800	Weak transcription	Fetal Kidney	kidney
31	chr11:77597800-77620000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:77597800-77624800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:77597800-77625000	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:77597800-77625000	Weak transcription	Pancreas	Pancrea
35	chr11:77597800-77625000	Weak transcription	NHDF-Ad	bronchial
36	chr11:77597800-77625200	Weak transcription	NHEK	skin
37	chr11:77597800-77625600	Weak transcription	HSMM	muscle
38	chr11:77597800-77629000	Weak transcription	Aorta	Aorta
39	chr11:77597800-77633800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:77597800-77644200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:77597800-77644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
44	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
47	chr11:77597800-77690000	Weak transcription	Gastric	stomach
48	chr11:77600200-77605800	Strong transcription	Fetal Muscle Leg	muscle
49	chr11:77600200-77606200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:77600200-77606200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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