Variant report

Variant	rs12528406
Chromosome Location	chr6:107040975-107040976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:107040171..107041861-chr6:107042293..107044623,2	MCF-7	breast:
2	chr6:107039605..107041440-chr6:107077353..107079327,2	K562	blood:

Variant related genes	Relation type
ENSG00000130348	Chromatin interaction
ENSG00000130347	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

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[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12524961	1.00[CHB][hapmap];0.83[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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12525436	1.00[CHB][hapmap];1.00[CHD][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527773	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12528136	0.89[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];1.00[MKK][hapmap];0.92[TSI][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]
rs12530128	1.00[LWK][hapmap]
rs12663120	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs17067217	0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs17067219	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs17067226	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs17067245	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17067371	1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs17067393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17067395	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]
rs17067428	0.88[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];1.00[MKK][hapmap];1.00[TSI][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[CHD][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];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs17067614	0.92[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	0.92[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:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12528406	TPBG	trans	brain	seeQTL
rs12528406	RTN4IP1	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
2	chr6:107010200-107064600	Weak transcription	A549	lung
3	chr6:107017800-107041000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:107018000-107052600	Weak transcription	Colonic Mucosa	Colon
5	chr6:107018400-107066400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:107018400-107076400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:107018800-107076200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:107019000-107076200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:107019800-107076400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:107022000-107076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:107023400-107050200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:107023400-107068800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:107023400-107076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:107029600-107052600	Weak transcription	Pancreas	Pancrea
15	chr6:107030800-107076800	Weak transcription	Small Intestine	intestine
16	chr6:107031200-107042200	Weak transcription	Esophagus	oesophagus
17	chr6:107031200-107052200	Weak transcription	Thymus	Thymus
18	chr6:107031200-107052600	Weak transcription	Gastric	stomach
19	chr6:107031200-107052800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:107031200-107058800	Weak transcription	Psoas Muscle	Psoas
21	chr6:107031200-107077000	Weak transcription	Spleen	Spleen
22	chr6:107031400-107048000	Weak transcription	Lung	lung
23	chr6:107031400-107065200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:107031400-107076200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:107031400-107076600	Weak transcription	Brain Angular Gyrus	brain
26	chr6:107031800-107076600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:107032600-107054000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:107033000-107076600	Weak transcription	Aorta	Aorta
29	chr6:107033200-107061000	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:107034400-107057400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:107035000-107047800	Weak transcription	Fetal Brain Male	brain
32	chr6:107035400-107076600	Weak transcription	Right Ventricle	heart
33	chr6:107035600-107054600	Weak transcription	Hela-S3	cervix
34	chr6:107035800-107070400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:107035800-107070400	Weak transcription	Fetal Lung	lung
36	chr6:107036000-107041200	Weak transcription	GM12878-XiMat	blood
37	chr6:107036000-107046600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:107036000-107051800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:107037200-107053800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:107039200-107042400	Weak transcription	Fetal Thymus	thymus
41	chr6:107039200-107076400	Weak transcription	Brain Germinal Matrix	brain
42	chr6:107039200-107076600	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:107039600-107041200	Weak transcription	NHEK	skin
44	chr6:107039600-107045000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr6:107039600-107046800	Weak transcription	Primary B cells from cord blood	blood
46	chr6:107039600-107052600	Weak transcription	Fetal Intestine Small	intestine
47	chr6:107039600-107076600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:107039600-107076600	Weak transcription	Fetal Stomach	stomach
49	chr6:107039800-107041800	Weak transcription	Fetal Brain Female	brain
50	chr6:107039800-107048800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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