Variant report

Variant	rs11079810
Chromosome Location	chr17:46227846-46227847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46177401..46179002-chr17:46225880..46228400,3	K562	blood:
2	chr17:46221592..46224484-chr17:46225566..46228411,3	K562	blood:
3	chr17:46104210..46106348-chr17:46226944..46229187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000005243	Chromatin interaction
ENSG00000108468	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11079813	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11650476	0.86[EUR][1000 genomes]
rs11650615	0.92[YRI][hapmap]
rs11654292	0.89[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11658242	0.88[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12103808	0.86[AMR][1000 genomes]
rs1544597	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1975703	0.89[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs28481675	0.86[EUR][1000 genomes]
rs56258199	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60707285	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60843764	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6504067	0.89[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6504114	0.89[CEU][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs6504115	0.88[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs7207553	0.89[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7207937	0.86[EUR][1000 genomes]
rs7210671	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7219844	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7220398	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7221720	0.86[AMR][1000 genomes]
rs7221897	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7222646	0.88[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7224155	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7225288	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73322881	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73322886	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73324779	0.86[EUR][1000 genomes]
rs8065797	0.89[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs8067470	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs8071697	0.89[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8073220	0.86[AMR][1000 genomes]
rs9890850	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9893110	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9894076	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9900074	0.85[YRI][hapmap]
rs9905800	0.88[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs9907268	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9909922	0.82[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11079810	RP5-890E16.2	cis	Nerve Tibial	GTEx
rs11079810	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:46211200-46231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:46212400-46234800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr17:46216600-46235600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr17:46220800-46228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:46221200-46228000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr17:46221400-46230800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:46221600-46238400	Weak transcription	Fetal Thymus	thymus
11	chr17:46222800-46234600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr17:46223200-46228400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:46225400-46228800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:46225400-46231600	Weak transcription	GM12878-XiMat	blood
15	chr17:46225600-46228000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:46225600-46229000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:46226000-46230800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:46226000-46230800	Weak transcription	Thymus	Thymus
19	chr17:46226200-46228000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr17:46226200-46230600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:46226200-46231400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:46226400-46228200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr17:46226400-46234600	Strong transcription	Primary T cells from cord blood	blood
24	chr17:46226600-46228800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
25	chr17:46226600-46229000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:46226600-46231800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:46226800-46230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:46227000-46228000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:46227000-46230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:46227000-46233600	Weak transcription	Spleen	Spleen
31	chr17:46227200-46228200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:46227200-46228400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr17:46227200-46228600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr17:46227200-46230600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:46227200-46230800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:46227400-46228600	Strong transcription	Liver	Liver

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