Variant report

Variant	rs1613945
Chromosome Location	chr11:77545808-77545809
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77545142..77547809-chr11:77555941..77558608,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10698394	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10793262	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793263	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10793264	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899398	0.83[EUR][1000 genomes]
rs10899402	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899403	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899405	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899406	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899407	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899408	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899409	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237284	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237289	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237295	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237299	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237303	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11518811	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12222530	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12364072	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12794428	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1783546	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790235	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1790240	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790246	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1793334	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793336	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793341	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2212317	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2298819	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2510967	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4245453	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4638330	0.81[EUR][1000 genomes]
rs4945198	0.85[EUR][1000 genomes]
rs4945201	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4945206	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs496786	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs574665	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61900164	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7110924	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7128224	0.82[EUR][1000 genomes]
rs7130719	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7358471	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7925343	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7927913	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7931272	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7940734	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9666484	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9988883	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1613945	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77533000-77553800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:77533000-77554000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:77533000-77554200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:77533400-77552200	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:77533400-77552200	Weak transcription	Left Ventricle	heart
6	chr11:77533400-77553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:77533400-77554000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:77533400-77565600	Weak transcription	Gastric	stomach
9	chr11:77533400-77565600	Weak transcription	Pancreas	Pancrea
10	chr11:77533600-77552200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:77533600-77553000	Weak transcription	HUVEC	blood vessel
12	chr11:77534600-77555400	Weak transcription	Lung	lung
13	chr11:77535200-77548800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:77535200-77551800	Weak transcription	Ovary	ovary
15	chr11:77535200-77552800	Weak transcription	Aorta	Aorta
16	chr11:77535200-77553800	Weak transcription	NHDF-Ad	bronchial
17	chr11:77535200-77554200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:77535200-77554400	Weak transcription	HSMM	muscle
19	chr11:77535400-77552000	Weak transcription	Fetal Intestine Large	intestine
20	chr11:77535400-77552200	Weak transcription	Liver	Liver
21	chr11:77535400-77553400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:77535400-77553400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:77535400-77554200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:77535400-77555000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:77535400-77565600	Weak transcription	HepG2	liver
26	chr11:77535800-77552000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:77535800-77552200	Weak transcription	Adipose Nuclei	Adipose
28	chr11:77535800-77552200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:77536600-77552200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:77541600-77553800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:77543000-77552200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:77543800-77549400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:77544600-77546600	Weak transcription	Fetal Stomach	stomach
34	chr11:77544600-77548800	Weak transcription	Fetal Lung	lung
35	chr11:77544600-77552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:77544600-77552400	Weak transcription	Psoas Muscle	Psoas
37	chr11:77544600-77552600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:77544600-77555400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:77544600-77564400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:77544600-77565400	Weak transcription	Spleen	Spleen
41	chr11:77544800-77547600	Weak transcription	Fetal Intestine Small	intestine
42	chr11:77544800-77548600	Weak transcription	Fetal Muscle Leg	muscle
43	chr11:77544800-77549200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:77544800-77549400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr11:77544800-77551800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:77544800-77552400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:77544800-77553400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:77544800-77554200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr11:77544800-77554200	Weak transcription	Dnd41	blood
50	chr11:77544800-77554400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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