Variant report

Variant	rs12525311
Chromosome Location	chr6:107026430-107026431
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	chr6:107026128..107027753-chr6:107075695..107078557,2	K562	blood:

Variant related genes	Relation type
ENSG00000130348	Chromatin interaction
ENSG00000130347	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10499046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12523666	0.92[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12523769	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12524955	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12524961	1.00[CHB][hapmap];0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs12525004	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[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12525583	0.92[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[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528406	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]
rs12529961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12530093	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]
rs12663120	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs17067217	0.92[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs17067219	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs17067226	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs17067245	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs17067371	1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs17067393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17067395	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]
rs17067428	0.88[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];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17067432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17067435	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[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];0.98[ASN][1000 genomes]
rs17067445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17067469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17067613	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs17067614	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1979347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2792467	0.83[ASN][1000 genomes]
rs3761800	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3804339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4363071	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4946766	0.98[ASN][1000 genomes]
rs56664576	0.98[ASN][1000 genomes]
rs56725742	0.98[ASN][1000 genomes]
rs58482231	0.98[ASN][1000 genomes]
rs58620450	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59480706	0.98[ASN][1000 genomes]
rs59962977	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6924412	0.89[EUR][1000 genomes]
rs6938201	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs72945007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945013	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945015	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945026	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945035	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945036	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945040	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945046	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945053	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945059	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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
rs12525311	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	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
2	chr6:106996400-107027000	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
5	chr6:106999800-107030600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:107008400-107027600	Strong transcription	Primary T cells from cord blood	blood
7	chr6:107010200-107064600	Weak transcription	A549	lung
8	chr6:107011800-107030000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:107012800-107030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:107014400-107038800	Weak transcription	Fetal Brain Female	brain
11	chr6:107016200-107039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:107017000-107032800	Weak transcription	K562	blood
13	chr6:107017800-107041000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:107018000-107030800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:107018000-107052600	Weak transcription	Colonic Mucosa	Colon
16	chr6:107018400-107066400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:107018400-107076400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:107018600-107029600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:107018600-107030000	Weak transcription	Fetal Intestine Large	intestine
20	chr6:107018600-107039000	Weak transcription	Placenta	Placenta
21	chr6:107018800-107030200	Weak transcription	Dnd41	blood
22	chr6:107018800-107039400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:107018800-107076200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:107019000-107029200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:107019000-107029400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:107019000-107029800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:107019000-107030200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:107019000-107030200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:107019000-107076200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:107019200-107029400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:107019200-107034800	Weak transcription	GM12878-XiMat	blood
32	chr6:107019400-107034400	Weak transcription	NHEK	skin
33	chr6:107019400-107035200	Weak transcription	Fetal Lung	lung
34	chr6:107019600-107029200	Weak transcription	Fetal Thymus	thymus
35	chr6:107019600-107029400	Weak transcription	Spleen	Spleen
36	chr6:107019800-107029000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:107019800-107076400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:107020200-107037600	Weak transcription	Fetal Heart	heart
39	chr6:107020400-107027200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:107020600-107029200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:107020600-107030600	Weak transcription	Thymus	Thymus
42	chr6:107020600-107032200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr6:107020800-107030000	Weak transcription	Esophagus	oesophagus
44	chr6:107021000-107029200	Weak transcription	Pancreas	Pancrea
45	chr6:107021600-107033400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:107022000-107076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr6:107022600-107026800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr6:107022600-107027800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr6:107023000-107030800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:107023200-107027000	Weak transcription	Osteobl	bone

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