Variant report

Variant	rs1322056
Chromosome Location	chr9:117672760-117672761
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	chr9:117423941..117424774-chr9:117672688..117673402,2	MCF-7	breast:
2	chr9:117500823..117501813-chr9:117672459..117674068,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230054	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1006025	0.82[EUR][1000 genomes]
rs1006026	0.94[EUR][1000 genomes]
rs1006027	0.82[EUR][1000 genomes]
rs10081728	0.83[EUR][1000 genomes]
rs10817679	0.90[ASN][1000 genomes]
rs10817682	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817683	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10817685	0.81[EUR][1000 genomes]
rs10982445	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982449	0.82[EUR][1000 genomes]
rs10982450	0.84[EUR][1000 genomes]
rs10982451	0.83[EUR][1000 genomes]
rs10982453	0.83[EUR][1000 genomes]
rs10982454	0.83[EUR][1000 genomes]
rs10982455	0.83[EUR][1000 genomes]
rs10982456	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1126711	0.96[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12337739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338765	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12347977	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12352646	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322058	0.83[EUR][1000 genomes]
rs1322060	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1322067	0.97[EUR][1000 genomes]
rs1407309	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17292087	0.84[EUR][1000 genomes]
rs2075533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181036	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2208640	0.83[EUR][1000 genomes]
rs2295800	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2418324	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2418325	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2974	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181195	0.84[EUR][1000 genomes]
rs3181197	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181200	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181201	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181202	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181348	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3181363	0.83[EUR][1000 genomes]
rs3181364	0.84[EUR][1000 genomes]
rs3181365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181366	0.84[EUR][1000 genomes]
rs3181367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181368	0.83[EUR][1000 genomes]
rs3181369	0.83[EUR][1000 genomes]
rs3181370	0.83[EUR][1000 genomes]
rs3181371	0.83[EUR][1000 genomes]
rs3181372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181374	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3789879	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978611	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979470	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4979471	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979472	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979473	0.84[EUR][1000 genomes]
rs6478117	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7025577	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7028578	0.84[EUR][1000 genomes]
rs7030090	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7032773	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7036962	0.83[EUR][1000 genomes]
rs7037640	0.84[EUR][1000 genomes]
rs726657	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7858603	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7872878	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs911603	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs927373	0.83[EUR][1000 genomes]
rs927374	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs927375	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[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	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117662200-117676200	Weak transcription	Gastric	stomach
2	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:117665800-117672800	Weak transcription	Spleen	Spleen
4	chr9:117667400-117673600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:117667600-117673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:117668800-117673400	Enhancers	Primary B cells from peripheral blood	blood
8	chr9:117668800-117673400	Enhancers	HMEC	breast
9	chr9:117669000-117674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr9:117669200-117673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:117669200-117673800	Enhancers	Fetal Thymus	thymus
12	chr9:117669800-117672800	Weak transcription	Fetal Stomach	stomach
13	chr9:117669800-117673600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr9:117670200-117673600	Enhancers	Osteobl	bone
15	chr9:117670400-117673400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:117670800-117673800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr9:117670800-117674200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:117670800-117687200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:117671000-117673000	Enhancers	Primary B cells from cord blood	blood
20	chr9:117671000-117673200	Genic enhancers	Primary T cells from cord blood	blood
21	chr9:117671000-117674600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:117671200-117672800	Weak transcription	Esophagus	oesophagus
23	chr9:117671200-117674200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr9:117671200-117676800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:117671400-117672800	Weak transcription	NHDF-Ad	bronchial
26	chr9:117671400-117673200	Weak transcription	NHLF	lung
27	chr9:117671400-117674000	Enhancers	Hela-S3	cervix
28	chr9:117671400-117674200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:117671600-117672800	Weak transcription	HSMMtube	muscle
30	chr9:117671600-117673000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:117671600-117673200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:117671600-117673400	Weak transcription	NH-A	brain
33	chr9:117671600-117674000	Enhancers	A549	lung
34	chr9:117671600-117675000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr9:117671800-117672800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:117671800-117672800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:117671800-117673200	Genic enhancers	Thymus	Thymus
38	chr9:117671800-117674800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:117671800-117676600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:117671800-117676800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr9:117672000-117674400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr9:117672000-117674400	Enhancers	Dnd41	blood
43	chr9:117672200-117672800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr9:117672200-117673000	Enhancers	Lung	lung
45	chr9:117672200-117673200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:117672200-117673200	Weak transcription	Fetal Lung	lung
47	chr9:117672200-117673400	Enhancers	Fetal Muscle Leg	muscle
48	chr9:117672200-117673600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:117672200-117676600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr9:117672400-117672800	Genic enhancers	Primary monocytes fromperipheralblood	blood

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