Variant report

Variant	rs11079811
Chromosome Location	chr17:46233490-46233491
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	chr17:46224894..46227721-chr17:46229708..46233601,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11079812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11868509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12449324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449529	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12601412	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12602010	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12948653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12953085	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16954750	0.81[YRI][hapmap]
rs17619103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2525103	0.84[CEU][hapmap]
rs34130316	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34449497	0.91[ASN][1000 genomes]
rs35371915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999311	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7215582	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7221416	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7224648	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11079811	PNPO	cis	cerebellum	SCAN
rs11079811	RPRML	cis	parietal	SCAN
rs11079811	NAGLU	cis	parietal	SCAN
rs11079811	PNPO	cis	parietal	SCAN
rs11079811	ASB16	cis	parietal	SCAN
rs11079811	KRT13	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:46212400-46234800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr17:46216600-46235600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:46221600-46238400	Weak transcription	Fetal Thymus	thymus
7	chr17:46222800-46234600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr17:46226400-46234600	Strong transcription	Primary T cells from cord blood	blood
9	chr17:46227000-46233600	Weak transcription	Spleen	Spleen
10	chr17:46228400-46236600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr17:46230200-46237400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:46230600-46245000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr17:46230800-46234200	Strong transcription	Thymus	Thymus
14	chr17:46231000-46236600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:46231000-46243800	Weak transcription	Primary B cells from cord blood	blood
16	chr17:46231400-46234200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:46231600-46234400	Strong transcription	GM12878-XiMat	blood
18	chr17:46231800-46233600	Weak transcription	Fetal Kidney	kidney
19	chr17:46231800-46233800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:46231800-46233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:46231800-46235200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:46231800-46238200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:46232000-46233800	Weak transcription	K562	blood
24	chr17:46232000-46236600	Weak transcription	A549	lung
25	chr17:46232000-46238000	Weak transcription	Pancreas	Pancrea
26	chr17:46232000-46239000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr17:46232000-46239800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr17:46232400-46237000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr17:46232600-46235400	Weak transcription	Fetal Intestine Large	intestine
30	chr17:46232800-46234600	Genic enhancers	Liver	Liver
31	chr17:46233000-46234000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr17:46233000-46234600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:46233200-46233600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
34	chr17:46233200-46233800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr17:46233200-46234000	Enhancers	Primary hematopoietic stem cells	blood
36	chr17:46233200-46234000	Enhancers	HSMMtube	muscle
37	chr17:46233200-46234200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr17:46233200-46234200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:46233200-46234200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:46233200-46234200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:46233200-46234200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:46233200-46234200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr17:46233200-46234200	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr17:46233200-46234400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:46233400-46233800	Bivalent Enhancer	Fetal Brain Female	brain
46	chr17:46233400-46234200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr17:46233400-46234200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:46233400-46234200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:46233400-46234400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr17:46233400-46234400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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