Variant report

Variant	rs7221720
Chromosome Location	chr17:46168892-46168893
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	chr17:46166805..46169680-chr17:46175249..46176872,2	K562	blood:
2	chr17:46168437..46170885-chr17:46173334..46176896,3	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11079810	0.86[AMR][1000 genomes]
rs11079813	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11654292	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11654342	0.82[AMR][1000 genomes]
rs11658242	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12103808	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1544597	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56258199	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60707285	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60843764	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6504067	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7207553	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7210671	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7219844	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7220398	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7221897	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7222646	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7224155	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7225288	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73322881	0.93[AMR][1000 genomes]
rs73322886	0.93[AMR][1000 genomes]
rs8065797	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8067470	0.82[AMR][1000 genomes]
rs8071697	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8073220	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9890850	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9893110	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9894076	0.85[AMR][1000 genomes]
rs9905800	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9907268	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9909922	0.86[AMR][1000 genomes];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7221720	SNX11	cis	brain	BrainEAC
rs7221720	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs7221720	SNX11	cis	temporal cortex	BrainEAC
rs7221720	SNX11	cis	frontal cortex	BrainEAC
rs7221720	SNX11	cis	hippocampus	BrainEAC

Chromatin state (count:111 , 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	chr17:46153400-46170800	Weak transcription	HSMM	muscle
8	chr17:46153800-46176800	Weak transcription	NHLF	lung
9	chr17:46154200-46176800	Weak transcription	HMEC	breast
10	chr17:46154200-46177600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr17:46154400-46170600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr17:46154400-46170800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr17:46154400-46170800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:46154400-46170800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:46154400-46171000	Weak transcription	HepG2	liver
16	chr17:46154400-46171200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:46154400-46171200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:46154400-46171200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr17:46154400-46171200	Weak transcription	Spleen	Spleen
20	chr17:46154400-46173000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:46154400-46176800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr17:46154400-46177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr17:46154400-46177200	Weak transcription	Placenta	Placenta
24	chr17:46154400-46177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr17:46154400-46177600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr17:46154400-46177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:46154400-46177600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr17:46154400-46177600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr17:46154400-46177600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:46154400-46177800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:46154600-46169600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:46154600-46170800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr17:46154600-46170800	Weak transcription	Fetal Brain Female	brain
34	chr17:46154600-46170800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr17:46154600-46171000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:46154600-46171000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr17:46154600-46171000	Weak transcription	Thymus	Thymus
38	chr17:46154600-46171200	Weak transcription	Fetal Intestine Large	intestine
39	chr17:46154600-46175400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr17:46154600-46176800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:46154600-46177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:46154600-46177000	Weak transcription	Osteobl	bone
43	chr17:46154600-46177600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr17:46155200-46169200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:46155200-46169800	Weak transcription	Fetal Thymus	thymus
46	chr17:46155200-46171600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr17:46155400-46171200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:46157600-46170600	Weak transcription	NHEK	skin
49	chr17:46163400-46175400	Weak transcription	Gastric	stomach
50	chr17:46163400-46175600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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