Variant report

Variant	rs869249
Chromosome Location	chr7:66387485-66387486
allele	C/T
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:66385651..66388919-chr7:66460114..66462403,3	MCF-7	breast:
2	chr7:66092683..66094985-chr7:66385486..66387762,2	K562	blood:
3	chr16:777428..780278-chr7:66386006..66387525,2	MCF-7	breast:
4	chr7:66386885..66388455-chr7:66393635..66395755,2	MCF-7	breast:
5	chr7:66204784..66206359-chr7:66385620..66388278,2	MCF-7	breast:
6	chr7:66309154..66310879-chr7:66385975..66387792,2	MCF-7	breast:
7	chr7:66308191..66311276-chr7:66384066..66387492,7	MCF-7	breast:
8	chr7:66385169..66388074-chr7:66392898..66397062,6	MCF-7	breast:
9	chr7:66384595..66388317-chr7:66459135..66463010,5	K562	blood:
10	chr7:66308297..66310076-chr7:66385373..66388075,2	K562	blood:
11	chr7:66378566..66381625-chr7:66385153..66387745,3	MCF-7	breast:
12	chr7:66118570..66121104-chr7:66386256..66388029,2	K562	blood:
13	chr7:66361028..66363688-chr7:66387186..66389228,2	K562	blood:
14	chr7:66379191..66382749-chr7:66384574..66388642,5	K562	blood:
15	chr7:66385188..66388317-chr7:66459133..66463010,3	K562	blood:
16	chr7:66312126..66314998-chr7:66385416..66387725,2	MCF-7	breast:
17	chr7:66384799..66388848-chr7:66389441..66396879,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198874	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000272831	Chromatin interaction
ENSG00000232546	Chromatin interaction
ENSG00000179131	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000103253	Chromatin interaction
ENSG00000106609	Chromatin interaction
ENSG00000126524	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000230583	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12698542	0.90[AFR][1000 genomes]
rs12698551	1.00[ASN][1000 genomes]
rs13228779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13229468	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13232393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13235282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13236129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13237544	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13238478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238612	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13246227	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1573944	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1880644	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1922723	0.90[AFR][1000 genomes]
rs2141924	0.90[AFR][1000 genomes]
rs2178742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2659903	0.90[AFR][1000 genomes]
rs2707823	0.90[AFR][1000 genomes]
rs2707826	0.82[AFR][1000 genomes]
rs2707828	0.80[AFR][1000 genomes]
rs2707830	0.90[AFR][1000 genomes]
rs34162778	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34314366	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34423980	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34559676	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34785430	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[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]
rs34816289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35043782	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35111158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35315599	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35390465	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35481333	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35508430	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35624856	0.88[ASN][1000 genomes]
rs35676956	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35821254	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35851021	0.88[ASN][1000 genomes]
rs35876551	0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36059333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457208	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849324	0.91[ASN][1000 genomes]
rs55889925	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006261	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56235846	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56675463	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs59308022	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs60201031	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60326618	0.90[AFR][1000 genomes]
rs66510832	0.83[ASN][1000 genomes]
rs67319329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71535634	0.85[ASN][1000 genomes]
rs71535635	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs71563136	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs876743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3324611	chr7:66383817-66388015	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs869249	ZNF117	cis	parietal	SCAN
rs869249	RP4-756H11.3	cis	lung	GTEx
rs869249	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs869249	GUSB	cis	Whole Blood	GTEx
rs869249	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs869249	ZNF117	cis	cerebellum	SCAN
rs869249	VKORC1L1	cis	parietal	SCAN
rs869249	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs869249	CRCP	cis	cerebellum	SCAN
rs869249	CRCP	cis	parietal	SCAN
rs869249	ASL	cis	multi-tissue	Pritchard
rs869249	ZNF273	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66385000-66388000	Active TSS	A549	lung
2	chr7:66385200-66387800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr7:66385400-66387600	Active TSS	Fetal Muscle Trunk	muscle
4	chr7:66385400-66387600	Active TSS	Thymus	Thymus
5	chr7:66385400-66388000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:66385400-66388200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr7:66385600-66387600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr7:66385600-66387600	Active TSS	Aorta	Aorta
9	chr7:66385600-66387600	Active TSS	Esophagus	oesophagus
10	chr7:66385600-66387600	Active TSS	Left Ventricle	heart
11	chr7:66385600-66387600	Active TSS	Lung	lung
12	chr7:66385600-66387600	Active TSS	Ovary	ovary
13	chr7:66385600-66387800	Active TSS	Fetal Intestine Small	intestine
14	chr7:66385600-66387800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr7:66385600-66387800	Active TSS	GM12878-XiMat	blood
16	chr7:66385800-66387600	Active TSS	Fetal Intestine Large	intestine
17	chr7:66386000-66387600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr7:66386000-66387600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:66386000-66387600	Active TSS	Gastric	stomach
20	chr7:66386200-66388200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:66386400-66387600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:66386600-66387600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr7:66386600-66387800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr7:66386600-66387800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr7:66386600-66387800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr7:66386600-66387800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:66386800-66387600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr7:66386800-66387600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:66386800-66387600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr7:66386800-66387600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr7:66386800-66387600	Flanking Active TSS	Hela-S3	cervix
32	chr7:66386800-66387800	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr7:66386800-66387800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:66386800-66387800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr7:66387000-66387600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr7:66387000-66387600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:66387000-66387600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:66387000-66387600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:66387000-66387600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr7:66387000-66387600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr7:66387000-66387600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr7:66387000-66387600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:66387000-66387600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr7:66387000-66387600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr7:66387000-66387600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:66387000-66387600	Flanking Active TSS	Liver	Liver
47	chr7:66387000-66387600	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr7:66387000-66387600	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr7:66387000-66387600	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr7:66387000-66387600	Flanking Active TSS	Brain Hippocampus Middle	brain

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