Variant report

Variant	rs679526
Chromosome Location	chr11:77597794-77597795
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs108843	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899401	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899414	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11237264	0.85[ASN][1000 genomes]
rs11237279	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12294668	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1783547	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2508184	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35711367	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs570786	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs581807	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582866	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs584732	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs585172	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs585721	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs591283	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598933	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600968	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs601551	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603462	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608389	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608539	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs609151	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs611671	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611906	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636041	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs647235	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs649671	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs658398	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs667213	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679155	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs685474	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694893	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925289	0.82[ASN][1000 genomes]
rs7929313	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7936105	0.95[ASN][1000 genomes]
rs9667706	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs679526	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr11:77578800-77601400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:77579200-77625000	Weak transcription	HMEC	breast
4	chr11:77579800-77597800	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr11:77580000-77597800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:77580800-77597800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:77582000-77598000	Strong transcription	Stomach Smooth Muscle	stomach
8	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
10	chr11:77584600-77597800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:77584800-77597800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:77585200-77597800	Strong transcription	Fetal Stomach	stomach
13	chr11:77586400-77597800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr11:77586600-77597800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:77586600-77597800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:77586600-77597800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:77586600-77625000	Weak transcription	Stomach Mucosa	stomach
18	chr11:77586800-77597800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:77587200-77617600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:77587600-77597800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:77587800-77603800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:77588200-77614000	Weak transcription	Right Ventricle	heart
23	chr11:77589200-77597800	Strong transcription	Thymus	Thymus
24	chr11:77589400-77597800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr11:77589600-77597800	Strong transcription	Fetal Intestine Small	intestine
26	chr11:77590600-77597800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:77590600-77597800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr11:77590600-77598000	Strong transcription	Fetal Thymus	thymus
29	chr11:77590600-77600800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:77590800-77597800	Strong transcription	Fetal Lung	lung
31	chr11:77591000-77597800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:77591000-77597800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:77591200-77605600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:77592400-77602400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:77592600-77600800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:77592800-77605400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
39	chr11:77593800-77625000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:77594000-77602000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr11:77595000-77600600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:77595000-77600800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:77595200-77600600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:77595200-77600800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:77595400-77620000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr11:77595600-77600600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:77595800-77600600	Weak transcription	Osteobl	bone
48	chr11:77595800-77600800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:77596000-77597800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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