Variant report

Variant	rs17067395
Chromosome Location	chr6:107030179-107030180
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	chr6:107028799..107031451-chr6:107035031..107036898,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10499046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12523666	0.92[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523769	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12524955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12524961	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs12525004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12525436	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12525583	0.94[ASN][1000 genomes]
rs12526024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527773	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12528136	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663120	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17067217	0.93[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs17067219	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17067226	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs17067245	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17067371	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs17067393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17067428	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17067432	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17067435	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17067443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17067445	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17067469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17067613	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs17067614	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17495248	0.86[AFR][1000 genomes]
rs17495623	0.86[AFR][1000 genomes]
rs17495742	0.86[AFR][1000 genomes]
rs1979347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2792467	0.81[ASN][1000 genomes]
rs3761800	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3804339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41292422	1.00[AFR][1000 genomes]
rs41312800	1.00[AFR][1000 genomes]
rs4363071	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4946766	0.96[ASN][1000 genomes]
rs55904932	1.00[AFR][1000 genomes]
rs56664576	1.00[ASN][1000 genomes]
rs56725742	1.00[ASN][1000 genomes]
rs58482231	0.96[ASN][1000 genomes]
rs58620450	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59480706	1.00[ASN][1000 genomes]
rs59962977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61741114	0.86[AFR][1000 genomes]
rs6924412	0.89[EUR][1000 genomes]
rs6938201	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs72941307	0.86[AFR][1000 genomes]
rs72941326	0.86[AFR][1000 genomes]
rs72943025	0.86[AFR][1000 genomes]
rs72943042	1.00[AFR][1000 genomes]
rs72943087	1.00[AFR][1000 genomes]
rs72943092	1.00[AFR][1000 genomes]
rs72943097	1.00[AFR][1000 genomes]
rs72945007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945008	1.00[AFR][1000 genomes]
rs72945013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945018	1.00[AFR][1000 genomes]
rs72945026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945029	1.00[AFR][1000 genomes]
rs72945030	1.00[AFR][1000 genomes]
rs72945035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945045	1.00[AFR][1000 genomes]
rs72945046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945053	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17067395	RTN4IP1	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
3	chr6:106999800-107030600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:107010200-107064600	Weak transcription	A549	lung
5	chr6:107012800-107030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:107014400-107038800	Weak transcription	Fetal Brain Female	brain
7	chr6:107016200-107039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:107017000-107032800	Weak transcription	K562	blood
9	chr6:107017800-107041000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:107018000-107030800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:107018000-107052600	Weak transcription	Colonic Mucosa	Colon
12	chr6:107018400-107066400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:107018400-107076400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:107018600-107039000	Weak transcription	Placenta	Placenta
15	chr6:107018800-107030200	Weak transcription	Dnd41	blood
16	chr6:107018800-107039400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:107018800-107076200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:107019000-107030200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:107019000-107030200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:107019000-107076200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:107019200-107034800	Weak transcription	GM12878-XiMat	blood
22	chr6:107019400-107034400	Weak transcription	NHEK	skin
23	chr6:107019400-107035200	Weak transcription	Fetal Lung	lung
24	chr6:107019800-107076400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:107020200-107037600	Weak transcription	Fetal Heart	heart
26	chr6:107020600-107030600	Weak transcription	Thymus	Thymus
27	chr6:107020600-107032200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:107021600-107033400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:107022000-107076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:107023000-107030800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:107023200-107030200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:107023200-107038200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr6:107023200-107038600	Weak transcription	Brain Germinal Matrix	brain
34	chr6:107023400-107030400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:107023400-107030800	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:107023400-107030800	Weak transcription	Lung	lung
37	chr6:107023400-107033200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:107023400-107034200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:107023400-107034200	Weak transcription	Right Ventricle	heart
40	chr6:107023400-107034400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:107023400-107034600	Weak transcription	Hela-S3	cervix
42	chr6:107023400-107038200	Weak transcription	HSMM	muscle
43	chr6:107023400-107038600	Weak transcription	NH-A	brain
44	chr6:107023400-107039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:107023400-107039600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:107023400-107050200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:107023400-107068800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:107023400-107076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:107023600-107030200	Weak transcription	Brain Angular Gyrus	brain
50	chr6:107023600-107030400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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