Variant report

Variant	rs3115631
Chromosome Location	chr6:29986324-29986325
allele	A/T
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: 12 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1264705	0.91[EUR][1000 genomes]
rs1264706	0.91[EUR][1000 genomes]
rs2023473	0.85[EUR][1000 genomes]
rs2517601	0.82[EUR][1000 genomes]
rs2523978	0.85[EUR][1000 genomes]
rs2844789	0.81[EUR][1000 genomes]
rs3094146	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9261290	1.00[AMR][1000 genomes];0.95[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3115631	ZFP57	cis	multi-tissue	Pritchard
rs3115631	HLA-A	cis	multi-tissue	Pritchard
rs3115631	HLA-G	cis	multi-tissue	Pritchard
rs3115631	HLA-A	cis	lymphoblastoid	GTEx
rs3115631	HLA-H	cis	multi-tissue	Pritchard
rs3115631	BTN3A2	cis	multi-tissue	Pritchard
rs3115631	HLA-A	cis	brain	seeQTL
rs3115631	HLA-DQA1	cis	multi-tissue	Pritchard
rs3115631	HLA-C	cis	multi-tissue	Pritchard
rs3115631	HLA-A	trans	brain	seeQTL

Chromatin state (count:68 , 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	chr6:29975600-29987200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:29975600-29987600	Weak transcription	HepG2	liver
5	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
6	chr6:29975800-29986600	Weak transcription	Esophagus	oesophagus
7	chr6:29975800-30027800	Weak transcription	Gastric	stomach
8	chr6:29976200-29986600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:29976200-29987800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:29976200-30001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:29976600-29987000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:29976600-29987800	Weak transcription	Adipose Nuclei	Adipose
13	chr6:29976600-30023000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:29976800-29990000	Weak transcription	NHLF	lung
15	chr6:29976800-30000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:29977000-30002000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:29977000-30002000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:29977200-29986600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:29977200-29987000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:29977200-29987200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:29977200-29987600	Weak transcription	Fetal Stomach	stomach
22	chr6:29977200-29988200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:29977200-29991200	Weak transcription	Placenta	Placenta
24	chr6:29977200-30000400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:29977200-30003800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:29977200-30024600	Weak transcription	Brain Anterior Caudate	brain
27	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
29	chr6:29977400-29987600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:29977400-29988000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:29977400-29990000	Weak transcription	Brain Germinal Matrix	brain
32	chr6:29977600-29987200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:29977800-29987000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:29977800-29987800	Weak transcription	Spleen	Spleen
35	chr6:29978000-29991400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:29978400-29986400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:29978400-29987600	Weak transcription	Brain Substantia Nigra	brain
38	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:29979400-30024600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:29979600-30022800	Weak transcription	Ovary	ovary
41	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
42	chr6:29980200-29987000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:29980200-30012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:29980400-29988600	Weak transcription	Fetal Brain Male	brain
45	chr6:29981200-30023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:29981600-29986800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:29981800-30010600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:29982400-29987200	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:29982400-29988000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr6:29982600-29988000	Weak transcription	GM12878-XiMat	blood

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