Variant report

Variant	rs7213339
Chromosome Location	chr17:46194802-46194803
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46188096..46189774-chr17:46193080..46195986,2	K562	blood:
2	chr17:46184571..46186273-chr17:46193637..46195242,2	MCF-7	breast:
3	chr17:46194453..46197293-chr17:46201950..46204423,2	MCF-7	breast:
4	chr17:46186937..46189774-chr17:46193080..46195996,3	K562	blood:

Variant related genes	Relation type
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1010228	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1010230	0.87[ASN][1000 genomes]
rs10853094	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11079806	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11079808	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11079809	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11649919	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11651097	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11655407	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869625	0.80[AMR][1000 genomes]
rs12450620	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12600980	0.90[ASN][1000 genomes]
rs12936731	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12939514	0.82[ASN][1000 genomes]
rs12941295	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12943543	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12946143	0.82[ASN][1000 genomes]
rs12949879	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12950213	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12950402	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12952163	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1452665	0.81[AMR][1000 genomes]
rs16951519	0.82[ASN][1000 genomes]
rs1860866	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2051821	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs208005	0.81[ASN][1000 genomes]
rs208008	0.83[ASN][1000 genomes]
rs208009	0.83[ASN][1000 genomes]
rs208019	0.81[ASN][1000 genomes]
rs2109983	0.87[ASN][1000 genomes]
rs2109984	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2229369	0.81[ASN][1000 genomes]
rs2240121	0.82[ASN][1000 genomes]
rs2285863	0.81[AMR][1000 genomes]
rs2325783	0.82[ASN][1000 genomes]
rs2325784	0.82[ASN][1000 genomes]
rs2325804	0.83[ASN][1000 genomes]
rs2325885	0.83[AMR][1000 genomes]
rs35361214	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35688835	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744346	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744347	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785737	0.86[ASN][1000 genomes]
rs3815472	0.83[ASN][1000 genomes]
rs4794441	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794448	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794449	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794450	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794451	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794453	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4995899	0.82[ASN][1000 genomes]
rs55920502	0.82[ASN][1000 genomes]
rs58203448	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58595405	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58624511	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62064953	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504024	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6504025	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6504031	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504032	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6847	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71356520	0.85[ASN][1000 genomes]
rs71356521	0.81[ASN][1000 genomes]
rs71369829	0.85[EUR][1000 genomes]
rs7209585	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7209730	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7212202	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7217496	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7218700	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7220520	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7221441	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7222136	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7224014	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7224461	0.87[ASN][1000 genomes]
rs741058	0.87[ASN][1000 genomes]
rs8065670	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8065993	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066049	0.87[ASN][1000 genomes]
rs8066391	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8069889	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8071199	0.92[ASN][1000 genomes]
rs8075500	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8076380	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8077860	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8078125	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8079616	0.83[ASN][1000 genomes]
rs8080662	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875065	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs875066	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9747001	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs978263	0.90[ASN][1000 genomes]
rs9807087	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9890691	0.90[ASN][1000 genomes]
rs9899275	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9899461	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9903692	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9909933	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9910516	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][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	esv1007058	chr17:46188741-46200367	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7213339	SNX11	cis	Whole Blood	GTEx
rs7213339	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs7213339	SNX11	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46185800-46195800	Weak transcription	Ovary	ovary
2	chr17:46186000-46195200	Weak transcription	Aorta	Aorta
3	chr17:46186000-46196200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr17:46186000-46198600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:46186200-46195000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:46186200-46195200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:46186200-46196200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:46186200-46198600	Weak transcription	Fetal Brain Male	brain
9	chr17:46186200-46203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:46186400-46195000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr17:46186400-46195000	Weak transcription	HSMM	muscle
12	chr17:46186400-46195000	Weak transcription	NHDF-Ad	bronchial
13	chr17:46186400-46195200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:46186400-46195400	Weak transcription	Brain Angular Gyrus	brain
15	chr17:46186400-46195400	Weak transcription	NH-A	brain
16	chr17:46186400-46196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr17:46186400-46196000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:46186400-46198600	Weak transcription	Small Intestine	intestine
19	chr17:46186400-46198800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr17:46186600-46195000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:46186600-46195200	Weak transcription	Stomach Mucosa	stomach
22	chr17:46186600-46196000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr17:46187600-46198400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr17:46188200-46195000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:46188200-46201200	Strong transcription	Fetal Intestine Small	intestine
26	chr17:46188200-46207400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr17:46188400-46195000	Weak transcription	Brain Substantia Nigra	brain
28	chr17:46188400-46201400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:46188600-46195000	Weak transcription	Pancreas	Pancrea
30	chr17:46188600-46196200	Weak transcription	Psoas Muscle	Psoas
31	chr17:46189000-46202600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:46189200-46197800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:46189200-46199000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr17:46189400-46198600	Strong transcription	Brain Anterior Caudate	brain
35	chr17:46189400-46204200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:46189600-46198800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:46189600-46200600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr17:46189600-46201800	Strong transcription	Fetal Muscle Leg	muscle
39	chr17:46189800-46202000	Strong transcription	Fetal Stomach	stomach
40	chr17:46190000-46201400	Strong transcription	Lung	lung
41	chr17:46190000-46204800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:46190200-46201600	Strong transcription	Liver	Liver
43	chr17:46190400-46196800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:46190400-46200600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr17:46190400-46201600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:46190400-46205000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:46190800-46196200	Weak transcription	Fetal Kidney	kidney
48	chr17:46190800-46196200	Weak transcription	Hela-S3	cervix
49	chr17:46190800-46201400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr17:46191000-46195000	Weak transcription	HMEC	breast

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