Variant report

Variant	rs7221897
Chromosome Location	chr17:46227076-46227077
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46224894..46227721-chr17:46229708..46233601,3	MCF-7	breast:
2	chr17:46177401..46179002-chr17:46225880..46228400,3	K562	blood:
3	chr17:46224844..46227376-chr17:46230087..46232594,2	MCF-7	breast:
4	chr17:46221592..46224484-chr17:46225566..46228411,3	K562	blood:
5	chr17:46104210..46106348-chr17:46226944..46229187,2	MCF-7	breast:
6	chr17:46222057..46223830-chr17:46225566..46227649,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX11-9	chr17:46227041-46227295	l_1463_chr17:46225690-46227295_whiteBloodCell

No data

Variant related genes	Relation type
ENSG00000005243	Chromatin interaction
ENSG00000108468	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11079810	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11079813	0.80[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11650476	0.87[EUR][1000 genomes]
rs11650615	0.88[YRI][hapmap]
rs11654292	0.82[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11654342	0.84[AMR][1000 genomes]
rs11658242	0.80[CEU][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes]
rs12103808	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1544597	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1975703	0.82[CEU][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs28481675	0.87[EUR][1000 genomes]
rs56258199	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60707285	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60843764	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6504067	0.82[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6504114	0.82[CEU][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs6504115	0.80[CEU][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs7207553	0.82[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7207937	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7210671	0.82[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7219844	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7220398	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7221720	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7222646	0.80[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7224155	0.80[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7225288	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73322881	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73322886	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73324779	0.87[EUR][1000 genomes]
rs8065797	0.82[CEU][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs8067470	0.80[CEU][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs8071697	0.82[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8073220	0.93[AMR][1000 genomes]
rs9890850	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9893110	0.82[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894076	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9900074	0.81[YRI][hapmap]
rs9905800	0.80[CEU][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes]
rs9907268	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909922	0.88[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
rs7221897	RP5-890E16.2	cis	Nerve Tibial	GTEx
rs7221897	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 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	chr17:46220800-46227200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr17:46220800-46228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:46221200-46228000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr17:46221400-46230800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:46221600-46238400	Weak transcription	Fetal Thymus	thymus
12	chr17:46222800-46234600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:46223200-46228400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:46224400-46227200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:46225400-46228800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:46225400-46231600	Weak transcription	GM12878-XiMat	blood
17	chr17:46225600-46228000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:46225600-46229000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:46226000-46227400	Weak transcription	Liver	Liver
20	chr17:46226000-46230800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:46226000-46230800	Weak transcription	Thymus	Thymus
22	chr17:46226200-46227200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
23	chr17:46226200-46228000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr17:46226200-46230600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr17:46226200-46231400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr17:46226400-46228200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr17:46226400-46234600	Strong transcription	Primary T cells from cord blood	blood
28	chr17:46226600-46227200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr17:46226600-46227200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
30	chr17:46226600-46227200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
31	chr17:46226600-46227400	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr17:46226600-46228800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
33	chr17:46226600-46229000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:46226600-46231800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr17:46226800-46227200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr17:46226800-46227200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:46226800-46227200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
38	chr17:46226800-46227400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr17:46226800-46227400	Bivalent Enhancer	Fetal Brain Male	brain
40	chr17:46226800-46230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:46227000-46227200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr17:46227000-46227200	Bivalent/Poised TSS	Fetal Brain Female	brain
43	chr17:46227000-46227200	Bivalent Enhancer	K562	blood
44	chr17:46227000-46228000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:46227000-46230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:46227000-46233600	Weak transcription	Spleen	Spleen

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