Variant report

Variant	rs9357092
Chromosome Location	chr6:29984252-29984253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-4	chr6:29979876-29989538	ENSG00000204623

Extended variants
information (count: 69 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10947050	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11752303	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12193100	0.84[EUR][1000 genomes]
rs12193110	0.81[EUR][1000 genomes]
rs12195207	0.85[EUR][1000 genomes]
rs12195260	0.86[EUR][1000 genomes]
rs12200084	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12202241	0.86[EUR][1000 genomes]
rs12206499	0.85[EUR][1000 genomes]
rs2071568	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2275855	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394247	0.80[EUR][1000 genomes]
rs2508035	0.84[EUR][1000 genomes]
rs2523935	0.81[EUR][1000 genomes]
rs33959627	0.87[AFR][1000 genomes]
rs35066870	0.87[EUR][1000 genomes]
rs35159526	0.87[EUR][1000 genomes]
rs3807031	0.87[AFR][1000 genomes]
rs3823352	0.86[EUR][1000 genomes]
rs3823353	0.85[EUR][1000 genomes]
rs3823354	0.86[EUR][1000 genomes]
rs3823355	0.86[EUR][1000 genomes]
rs3823358	0.87[EUR][1000 genomes]
rs3823369	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3910312	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4248141	0.80[EUR][1000 genomes]
rs4248142	0.80[EUR][1000 genomes]
rs4248143	0.80[EUR][1000 genomes]
rs4711206	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711207	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711209	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713269	0.80[EUR][1000 genomes]
rs4713270	0.80[EUR][1000 genomes]
rs4713274	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713275	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4713279	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713281	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947244	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959010	0.88[EUR][1000 genomes]
rs4959038	0.80[EUR][1000 genomes]
rs4959039	0.93[EUR][1000 genomes]
rs4959040	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6457127	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903753	0.88[EUR][1000 genomes]
rs6904029	0.88[EUR][1000 genomes]
rs6916422	0.85[EUR][1000 genomes]
rs6916451	0.85[EUR][1000 genomes]
rs6935024	0.80[EUR][1000 genomes]
rs7766469	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295825	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295826	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295829	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295830	0.83[AFR][1000 genomes]
rs9348835	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357088	0.84[EUR][1000 genomes]
rs9366750	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9366752	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378141	0.80[EUR][1000 genomes]
rs9378142	0.84[EUR][1000 genomes]
rs9380150	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393984	0.83[EUR][1000 genomes]
rs9393986	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393987	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393988	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393989	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9405044	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9357092	NDUFS1	trans	multi-tissue	Pritchard
rs9357092	KIT	trans	multi-tissue	Pritchard
rs9357092	TFG	trans	multi-tissue	Pritchard
rs9357092	BTN2A1	cis	cerebellum	SCAN
rs9357092	HLA-F	cis	multi-tissue	Pritchard
rs9357092	HIST1H2AH	cis	cerebellum	SCAN
rs9357092	HLA-H	cis	lymphoblastoid	seeQTL
rs9357092	HLA-A	cis	lymphoblastoid	seeQTL
rs9357092	HLA-A	cis	brain	seeQTL
rs9357092	HLA-G	cis	multi-tissue	Pritchard
rs9357092	HLA-A	cis	multi-tissue	Pritchard
rs9357092	HLA-H	cis	multi-tissue	Pritchard
rs9357092	HLA-L	cis	lymphoblastoid	seeQTL
rs9357092	HLA.A29.1	cis	multi-tissue	Pritchard
rs9357092	HCG2P7	cis	multi-tissue	Pritchard
rs9357092	TPD52L2	trans	multi-tissue	Pritchard
rs9357092	HCG4	cis	multi-tissue	Pritchard
rs9357092	HIST1H2AI	cis	parietal	SCAN
rs9357092	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29974800-30002400	Weak transcription	Dnd41	blood
2	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
3	chr6:29975400-29985200	Weak transcription	Lung	lung
4	chr6:29975600-29985000	Weak transcription	Liver	Liver
5	chr6:29975600-29985200	Weak transcription	Primary B cells from cord blood	blood
6	chr6:29975600-29987200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:29975600-29987600	Weak transcription	HepG2	liver
8	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
9	chr6:29975800-29986600	Weak transcription	Esophagus	oesophagus
10	chr6:29975800-30027800	Weak transcription	Gastric	stomach
11	chr6:29976200-29986600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:29976200-29987800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:29976200-30001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:29976600-29987000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:29976600-29987800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:29976600-30023000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:29976800-29985800	Weak transcription	Left Ventricle	heart
18	chr6:29976800-29990000	Weak transcription	NHLF	lung
19	chr6:29976800-30000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:29977000-30002000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:29977000-30002000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:29977200-29985600	Weak transcription	Primary T cells from cord blood	blood
23	chr6:29977200-29986600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:29977200-29987000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:29977200-29987200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:29977200-29987600	Weak transcription	Fetal Stomach	stomach
27	chr6:29977200-29988200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:29977200-29991200	Weak transcription	Placenta	Placenta
29	chr6:29977200-30000400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:29977200-30003800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:29977200-30024600	Weak transcription	Brain Anterior Caudate	brain
32	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:29977400-29987600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:29977400-29988000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:29977400-29990000	Weak transcription	Brain Germinal Matrix	brain
37	chr6:29977600-29987200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:29977800-29987000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:29977800-29987800	Weak transcription	Spleen	Spleen
40	chr6:29978000-29985200	Weak transcription	Thymus	Thymus
41	chr6:29978000-29991400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:29978400-29986400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:29978400-29987600	Weak transcription	Brain Substantia Nigra	brain
44	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:29979400-30024600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:29979600-30022800	Weak transcription	Ovary	ovary
47	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
48	chr6:29980200-29987000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:29980200-30012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:29980400-29988600	Weak transcription	Fetal Brain Male	brain

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