Variant report

Variant	rs56258199
Chromosome Location	chr17:46183246-46183247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
2	chr17:46124892..46127654-chr17:46182877..46187326,5	K562	blood:
3	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
4	chr17:46177349..46180853-chr17:46182060..46186447,10	K562	blood:

Variant related genes	Relation type
ENSG00000002919	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000263412	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11079810	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11079813	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11650476	0.81[EUR][1000 genomes]
rs11654292	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11654342	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11658242	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12103808	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1544597	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1975703	0.81[EUR][1000 genomes]
rs28481675	0.81[EUR][1000 genomes]
rs60707285	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60843764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6504067	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6504114	0.81[EUR][1000 genomes]
rs6504115	0.81[EUR][1000 genomes]
rs7207553	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7207937	0.80[AMR][1000 genomes]
rs7210671	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7219844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7220398	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7221720	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7221897	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7222646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7224155	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7225288	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73322881	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73322886	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73324779	0.81[EUR][1000 genomes]
rs8065797	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8067470	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8071697	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8073220	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9890850	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9893110	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9894076	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9905800	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9907268	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9909922	0.91[AMR][1000 genomes];0.90[EUR][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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv112217	chr17:46182711-46190093	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56258199	RP5-890E16.2	cis	Nerve Tibial	GTEx
rs56258199	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46178400-46184200	Weak transcription	Fetal Heart	heart
2	chr17:46179200-46183800	Weak transcription	Brain Hippocampus Middle	brain
3	chr17:46179200-46184000	Weak transcription	Spleen	Spleen
4	chr17:46179200-46184000	Weak transcription	HepG2	liver
5	chr17:46179200-46184200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr17:46179200-46184200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:46179200-46184200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:46179200-46184200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:46179200-46184200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr17:46179200-46184200	Weak transcription	Left Ventricle	heart
11	chr17:46179200-46184200	Weak transcription	Pancreas	Pancrea
12	chr17:46179200-46184200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:46179200-46184400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:46179400-46183800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:46179400-46184000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr17:46179400-46184200	Weak transcription	Primary T cells from cord blood	blood
17	chr17:46179400-46184200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:46179400-46184200	Weak transcription	Colonic Mucosa	Colon
19	chr17:46179400-46184200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr17:46179400-46184200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr17:46179600-46183800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:46179600-46184000	Weak transcription	Liver	Liver
23	chr17:46179600-46184000	Weak transcription	Dnd41	blood
24	chr17:46179600-46184000	Weak transcription	Hela-S3	cervix
25	chr17:46179600-46184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:46179600-46184200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:46179600-46184200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:46179600-46184200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:46179600-46184200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr17:46179600-46184200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:46179600-46184200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr17:46179600-46184200	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:46179600-46184200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr17:46179600-46184200	Weak transcription	NHEK	skin
35	chr17:46179600-46184400	Weak transcription	NHDF-Ad	bronchial
36	chr17:46179800-46184400	Weak transcription	Small Intestine	intestine
37	chr17:46181000-46183600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr17:46181000-46183800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr17:46181000-46184000	Weak transcription	Fetal Thymus	thymus
40	chr17:46181000-46184200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr17:46181000-46184200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr17:46181200-46183600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr17:46181200-46184200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr17:46181200-46184200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr17:46181400-46183600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr17:46181400-46183600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:46181800-46183400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr17:46181800-46183600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr17:46181800-46183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr17:46182200-46183600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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