Variant report

Variant	rs9895554
Chromosome Location	chr17:46123642-46123643
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr17:46121714-46126967	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:46122734-46126909	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr17:46122485-46124228	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr17:46123586-46123834	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr17:46122512-46124013	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:46123447-46126752	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr17:46121736-46126744	K562	blood:	n/a	n/a
8	JUN	chr17:46122472-46126784	K562	blood:	n/a	chr17:46125601-46125610 chr17:46125499-46125508 chr17:46124562-46124569 chr17:46124562-46124571 chr17:46125676-46125685 chr17:46124353-46124365

No.	Distal block	Cell Line	Cell type
1	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
2	chr17:46120800..46123915-chr17:46177973..46180193,3	MCF-7	breast:
3	chr17:46052757..46054496-chr17:46123061..46125014,2	K562	blood:
4	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
5	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPZ2-1	chr17:46122503-46125412	ENSG00000263412.1

Variant related genes	Relation type
NFE2L1	TF binding region
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10491182	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10491183	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1051001	0.98[EUR][1000 genomes]
rs11079805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11650043	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs11650615	0.83[LWK][hapmap];0.95[MKK][hapmap];0.88[YRI][hapmap]
rs11651275	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11656818	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11658242	0.83[YRI][hapmap]
rs12452399	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16969990	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs17617360	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs17618704	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs17679445	1.00[CEU][hapmap]
rs28405789	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35091825	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41429650	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4378657	0.82[GIH][hapmap]
rs7209072	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7210041	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7210671	0.83[YRI][hapmap]
rs9890096	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9900074	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903963	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9914123	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9895554	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs9895554	SNX11	cis	multi-tissue	Pritchard
rs9895554	RP5-890E16.2	cis	Nerve Tibial	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46115600-46123800	Weak transcription	Brain Substantia Nigra	brain
2	chr17:46116000-46124000	Weak transcription	Brain Hippocampus Middle	brain
3	chr17:46119400-46123800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:46120600-46124200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:46120600-46124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:46121800-46124400	Enhancers	Fetal Muscle Leg	muscle
7	chr17:46122400-46124000	Weak transcription	Primary T cells from cord blood	blood
8	chr17:46122400-46124200	Enhancers	Fetal Muscle Trunk	muscle
9	chr17:46122400-46124400	Enhancers	Adipose Nuclei	Adipose
10	chr17:46122600-46124000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr17:46122600-46124000	Enhancers	Esophagus	oesophagus
12	chr17:46122600-46124000	Enhancers	HMEC	breast
13	chr17:46122600-46124200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:46122600-46124200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:46122600-46124400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:46122600-46124800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:46122600-46124800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr17:46122600-46124800	Flanking Active TSS	HSMM	muscle
19	chr17:46122600-46125000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:46122800-46123800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:46122800-46123800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr17:46122800-46123800	Enhancers	Hela-S3	cervix
23	chr17:46122800-46124000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:46122800-46124000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr17:46122800-46124000	Enhancers	Fetal Heart	heart
26	chr17:46122800-46124200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:46122800-46124200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:46122800-46124200	Enhancers	Fetal Thymus	thymus
29	chr17:46122800-46124200	Enhancers	Stomach Smooth Muscle	stomach
30	chr17:46122800-46124400	Enhancers	Colonic Mucosa	Colon
31	chr17:46122800-46124400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr17:46122800-46124400	Enhancers	Right Atrium	heart
33	chr17:46122800-46124600	Enhancers	Pancreas	Pancrea
34	chr17:46122800-46124600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr17:46122800-46124600	Enhancers	HepG2	liver
36	chr17:46122800-46124800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:46122800-46125000	Flanking Active TSS	NHEK	skin
38	chr17:46123000-46124000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr17:46123000-46124000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr17:46123000-46124000	Weak transcription	Brain Anterior Caudate	brain
41	chr17:46123000-46124200	Enhancers	Primary B cells from cord blood	blood
42	chr17:46123000-46124200	Enhancers	Brain Germinal Matrix	brain
43	chr17:46123000-46124200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr17:46123000-46124400	Enhancers	Fetal Intestine Small	intestine
45	chr17:46123000-46124600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr17:46123000-46124800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:46123200-46123800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr17:46123200-46123800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:46123200-46124000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:46123200-46124000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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