Variant report

Variant	rs9890850
Chromosome Location	chr17:46172120-46172121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46171139..46172975-chr17:46176527..46178517,2	MCF-7	breast:
2	chr17:46123863..46127631-chr17:46170882..46172676,3	MCF-7	breast:

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

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11079810	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11079813	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11650476	0.81[EUR][1000 genomes]
rs11654292	0.93[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	0.89[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]
rs56258199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60707285	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60843764	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6504067	0.95[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	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7207937	0.80[AMR][1000 genomes]
rs7210671	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7219844	0.98[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	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7221897	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7222646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7224155	0.81[AFR][1000 genomes];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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8073220	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9893110	0.81[AFR][1000 genomes];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:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9890850	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs9890850	RP5-890E16.2	cis	Nerve Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46144800-46177800	Weak transcription	Right Ventricle	heart
2	chr17:46147800-46177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:46149000-46178000	Weak transcription	Lung	lung
4	chr17:46152400-46177200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:46152600-46176800	Weak transcription	K562	blood
6	chr17:46152600-46177000	Weak transcription	HSMMtube	muscle
7	chr17:46153800-46176800	Weak transcription	NHLF	lung
8	chr17:46154200-46176800	Weak transcription	HMEC	breast
9	chr17:46154200-46177600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr17:46154400-46173000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:46154400-46176800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:46154400-46177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr17:46154400-46177200	Weak transcription	Placenta	Placenta
14	chr17:46154400-46177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:46154400-46177600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr17:46154400-46177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:46154400-46177600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:46154400-46177600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:46154400-46177600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:46154400-46177800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:46154600-46175400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:46154600-46176800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:46154600-46177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:46154600-46177000	Weak transcription	Osteobl	bone
25	chr17:46154600-46177600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr17:46163400-46175400	Weak transcription	Gastric	stomach
27	chr17:46163400-46175600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr17:46163400-46177600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr17:46163600-46177200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr17:46163600-46177600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr17:46163800-46173000	Weak transcription	GM12878-XiMat	blood
32	chr17:46163800-46175200	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:46163800-46175200	Weak transcription	Hela-S3	cervix
34	chr17:46163800-46175400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr17:46163800-46176800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr17:46163800-46176800	Weak transcription	Brain Angular Gyrus	brain
37	chr17:46163800-46176800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr17:46163800-46177000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:46163800-46177200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr17:46163800-46177600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr17:46163800-46177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr17:46163800-46177600	Weak transcription	Stomach Mucosa	stomach
43	chr17:46163800-46177800	Weak transcription	Pancreas	Pancrea
44	chr17:46164000-46172400	Weak transcription	NH-A	brain
45	chr17:46164000-46172800	Weak transcription	Primary T cells from cord blood	blood
46	chr17:46164000-46175200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr17:46164000-46175400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr17:46164000-46177000	Weak transcription	Fetal Lung	lung
49	chr17:46164000-46177200	Weak transcription	Ovary	ovary
50	chr17:46164200-46175200	Weak transcription	Fetal Heart	heart

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