Variant report

Variant	rs2039826
Chromosome Location	chr10:99526668-99526669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99472748..99475606-chr10:99525832..99527526,2	K562	blood:
2	chr10:99414536..99416149-chr10:99526042..99527774,2	MCF-7	breast:
3	chr10:99524037..99526896-chr10:99538605..99541496,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155254	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10748709	0.80[ASN][1000 genomes]
rs10786367	0.85[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs10786370	0.85[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs10786371	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs10786372	0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10786373	0.82[ASN][1000 genomes]
rs10786374	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882993	0.80[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs10882995	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882996	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882997	0.84[EUR][1000 genomes]
rs11189350	0.85[ASN][1000 genomes]
rs11189352	0.86[ASN][1000 genomes]
rs11189353	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs11189355	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189356	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11189357	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11189359	0.89[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11189360	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189361	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11189362	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11189367	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189374	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189376	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189377	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11591898	0.89[ASN][1000 genomes]
rs11597378	0.94[CHB][hapmap]
rs12412543	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569711	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569757	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12780534	0.86[ASN][1000 genomes]
rs12783992	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1538723	0.89[ASN][1000 genomes]
rs1556971	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1981237	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs1981238	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34283185	0.84[EUR][1000 genomes]
rs3750612	0.94[CEU][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3750614	0.82[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs3750615	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3814558	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs3814559	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs3814560	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs4244329	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs4244330	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917784	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4917785	0.83[ASN][1000 genomes]
rs4917786	0.82[AMR][1000 genomes]
rs4919139	0.83[CEU][hapmap];0.82[ASN][1000 genomes]
rs7080894	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs7080953	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7081361	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7081652	0.82[ASN][1000 genomes]
rs7099540	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7100453	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7478323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907679	0.85[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs7910589	0.80[ASN][1000 genomes]
rs7916164	0.88[EUR][1000 genomes]
rs7916454	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs7922907	0.94[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs883324	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs946777	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs946778	0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2039826	AVPI1	cis	multi-tissue	Pritchard
rs2039826	ZFYVE27	cis	cerebellum	SCAN
rs2039826	DHDPSL	cis	cerebellum	SCAN
rs2039826	AVPI1	cis	Liver	GTEx
rs2039826	ZFYVE27	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99520000-99527800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr10:99520200-99528400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:99520400-99529200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:99520400-99530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr10:99520600-99528400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr10:99521600-99528200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr10:99522200-99528000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:99522200-99530800	Weak transcription	Right Ventricle	heart
9	chr10:99522400-99526800	Weak transcription	NHLF	lung
10	chr10:99522400-99527000	Weak transcription	NHEK	skin
11	chr10:99522400-99527400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr10:99522400-99527600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:99522400-99528200	Weak transcription	Aorta	Aorta
14	chr10:99522400-99528400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:99522400-99529000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr10:99522400-99530200	Weak transcription	A549	lung
17	chr10:99522600-99527000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr10:99522600-99527000	Weak transcription	Esophagus	oesophagus
19	chr10:99522600-99527000	Weak transcription	Gastric	stomach
20	chr10:99522600-99527600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr10:99522600-99528400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr10:99522600-99530000	Weak transcription	Fetal Intestine Large	intestine
23	chr10:99522600-99530400	Weak transcription	Primary T cells from cord blood	blood
24	chr10:99522800-99528200	Weak transcription	Colonic Mucosa	Colon
25	chr10:99522800-99529400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr10:99523000-99527000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:99523000-99527200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr10:99523000-99527800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:99523200-99526800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr10:99523200-99527600	Weak transcription	Lung	lung
31	chr10:99523200-99527800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr10:99523200-99528200	Weak transcription	Brain Germinal Matrix	brain
33	chr10:99523200-99530400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:99523400-99527000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:99523400-99528000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr10:99523400-99529000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr10:99523600-99528000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr10:99523600-99528800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr10:99524200-99527600	Weak transcription	Brain Substantia Nigra	brain
40	chr10:99524200-99530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr10:99524600-99527400	Weak transcription	Spleen	Spleen
42	chr10:99524600-99527600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr10:99524600-99528200	Weak transcription	Primary B cells from cord blood	blood
44	chr10:99524600-99528800	Weak transcription	Thymus	Thymus
45	chr10:99524800-99529200	Weak transcription	GM12878-XiMat	blood
46	chr10:99525000-99530400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr10:99525200-99527200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr10:99525200-99527200	Weak transcription	Pancreas	Pancrea
49	chr10:99525200-99527400	Weak transcription	Placenta	Placenta
50	chr10:99525400-99529000	Weak transcription	Duodenum Mucosa	Duodenum

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