Variant report

Variant	rs6927012
Chromosome Location	chr6:26471992-26471993
allele	A/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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26464821..26467283-chr6:26470555..26474076,4	MCF-7	breast:
2	chr6:26467959..26470668-chr6:26470770..26473697,4	MCF-7	breast:
3	chr6:26471471..26473302-chr6:26536499..26539408,2	K562	blood:
4	chr6:26432568..26435135-chr6:26469851..26472610,2	K562	blood:
5	chr6:26471319..26475410-chr6:26567164..26571952,5	K562	blood:
6	chr6:26470620..26472220-chr6:26474706..26477657,2	MCF-7	breast:
7	chr6:26470613..26473867-chr6:26476951..26479626,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF322-2	chr6:26471519-26472421	NONHSAT147385

No data

Variant related genes	Relation type
ENSG00000112763	Chromatin interaction
ENSG00000182952	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1535278	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15580	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes]
rs1796519	0.80[CEU][hapmap]
rs1796524	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2145319	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2224379	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3736780	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3864291	1.00[JPT][hapmap]
rs4713007	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes]
rs6905163	0.83[AMR][1000 genomes]
rs6911330	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6929908	0.86[MKK][hapmap]
rs7745632	1.00[CEU][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap]
rs9366661	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6927012	RP11-457M11.5	cis	Artery Aorta	GTEx
rs6927012	RP11-457M11.5	cis	lung	GTEx
rs6927012	RP11-457M11.5	cis	Thyroid	GTEx
rs6927012	RP11-457M11.5	cis	Adipose Subcutaneous	GTEx
rs6927012	RP11-457M11.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26462000-26472000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:26466600-26473800	Weak transcription	Fetal Heart	heart
3	chr6:26467200-26472800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:26467200-26473800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:26469000-26473200	Weak transcription	Hela-S3	cervix
6	chr6:26469200-26472800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:26469400-26473800	Weak transcription	Ovary	ovary
8	chr6:26469600-26473000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:26469600-26473200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:26469600-26473200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:26469600-26473200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:26469600-26473200	Weak transcription	K562	blood
13	chr6:26469600-26473200	Weak transcription	NHLF	lung
14	chr6:26469600-26473400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:26469600-26473400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:26469600-26473400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:26469600-26473400	Weak transcription	HMEC	breast
18	chr6:26469600-26473400	Weak transcription	HSMMtube	muscle
19	chr6:26469600-26473400	Weak transcription	HUVEC	blood vessel
20	chr6:26469600-26473400	Weak transcription	NHEK	skin
21	chr6:26469600-26473400	Weak transcription	Osteobl	bone
22	chr6:26469600-26473600	Weak transcription	A549	lung
23	chr6:26469600-26473800	Weak transcription	Brain Angular Gyrus	brain
24	chr6:26469600-26473800	Weak transcription	Brain Anterior Caudate	brain
25	chr6:26469600-26473800	Weak transcription	Placenta	Placenta
26	chr6:26469600-26473800	Weak transcription	Right Ventricle	heart
27	chr6:26469600-26474000	Weak transcription	HSMM	muscle
28	chr6:26469600-26474200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:26469600-26476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:26469800-26472200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:26469800-26473200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:26469800-26473400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:26469800-26473800	Weak transcription	Fetal Brain Female	brain
34	chr6:26469800-26473800	Weak transcription	NH-A	brain
35	chr6:26470000-26472000	Weak transcription	Dnd41	blood
36	chr6:26470000-26472800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:26470200-26472800	Weak transcription	Liver	Liver
38	chr6:26470200-26473400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:26470400-26472800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:26470400-26473400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:26470400-26473800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:26470400-26473800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:26470800-26472000	Strong transcription	Primary T cells from cord blood	blood
44	chr6:26471000-26473800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:26471200-26472200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:26471200-26473200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:26471400-26472000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:26471400-26472600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:26471400-26472800	ZNF genes & repeats	Primary B cells from cord blood	blood
50	chr6:26471400-26473200	Weak transcription	NHDF-Ad	bronchial

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