Variant report

Variant	rs1790339
Chromosome Location	chr11:71182761-71182762
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:71166959..71169196-chr11:71181524..71183295,2	MCF-7	breast:
2	chr11:71182002..71184181-chr11:71185465..71188579,3	K562	blood:
3	chr11:71180625..71183192-chr11:71184485..71186418,2	MCF-7	breast:
4	chr11:71163024..71164713-chr11:71182379..71183959,2	MCF-7	breast:
5	chr11:71176676..71180057-chr11:71180223..71183173,4	MCF-7	breast:
6	chr11:71177769..71179272-chr11:71180854..71183536,2	K562	blood:

Variant related genes	Relation type
ENSG00000172890	Chromatin interaction
ENSG00000172893	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10898144	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1123007	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12224205	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1540127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630498	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790324	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790328	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790330	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790341	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790343	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790345	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1790350	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790353	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792233	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792264	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1792277	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792280	0.92[ASN][1000 genomes]
rs1792281	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1792282	0.85[ASN][1000 genomes]
rs1792283	0.84[ASN][1000 genomes]
rs1792284	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1792315	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002064	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276358	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2511010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794057	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736894	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1052432	chr11:71167449-71213007	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1790339	RP11-660L16.2	cis	Whole Blood	GTEx
rs1790339	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1790339	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs1790339	NADSYN1	cis	Nerve Tibial	GTEx
rs1790339	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs1790339	RP11-660L16.2	cis	Artery Aorta	GTEx
rs1790339	RP11-660L16.2	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
2	chr11:71165200-71199200	Weak transcription	Right Atrium	heart
3	chr11:71165400-71194200	Weak transcription	Fetal Heart	heart
4	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:71166000-71194200	Weak transcription	Fetal Brain Male	brain
6	chr11:71167400-71194000	Weak transcription	Fetal Kidney	kidney
7	chr11:71170600-71184600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr11:71170600-71187600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:71171000-71183600	Weak transcription	Fetal Lung	lung
10	chr11:71171000-71184000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:71171000-71184200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:71171400-71184200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:71171400-71184200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:71171400-71184200	Weak transcription	NH-A	brain
15	chr11:71171600-71183600	Weak transcription	Small Intestine	intestine
16	chr11:71171600-71194000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:71171800-71189000	Weak transcription	Stomach Mucosa	stomach
18	chr11:71172200-71195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:71173000-71183000	Weak transcription	Osteobl	bone
20	chr11:71173200-71184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:71174800-71183800	Weak transcription	HMEC	breast
22	chr11:71175200-71183000	Weak transcription	Hela-S3	cervix
23	chr11:71175400-71183000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:71176400-71182800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:71177800-71188400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:71178000-71184400	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:71178200-71183400	Weak transcription	NHLF	lung
28	chr11:71178400-71182800	Weak transcription	HepG2	liver
29	chr11:71178400-71183000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:71178400-71183200	Weak transcription	Brain Germinal Matrix	brain
31	chr11:71178400-71183200	Weak transcription	Fetal Thymus	thymus
32	chr11:71178400-71183200	Weak transcription	Pancreas	Pancrea
33	chr11:71178400-71183800	Weak transcription	Right Ventricle	heart
34	chr11:71178400-71192600	Weak transcription	K562	blood
35	chr11:71178600-71183000	Weak transcription	Ovary	ovary
36	chr11:71178600-71183000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:71178800-71182800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:71179000-71182800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:71179000-71183000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:71179000-71183000	Weak transcription	Dnd41	blood
41	chr11:71179000-71183000	Weak transcription	HSMM	muscle
42	chr11:71179000-71183000	Weak transcription	HUVEC	blood vessel
43	chr11:71179000-71183000	Weak transcription	NHDF-Ad	bronchial
44	chr11:71179200-71183000	Weak transcription	NHEK	skin
45	chr11:71179600-71183200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:71179600-71190400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:71180000-71183200	Weak transcription	A549	lung
48	chr11:71180400-71183000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:71180400-71183200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:71180400-71184800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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