Variant report

Variant	rs2780975
Chromosome Location	chr9:86244989-86244990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86244611..86247023-chr9:86320465..86322962,2	MCF-7	breast:
2	chr9:86244110..86246714-chr9:86535414..86538304,2	K562	blood:
3	chr9:86238599..86242233-chr9:86242446..86245459,4	K562	blood:
4	chr9:86243220..86245781-chr9:86323093..86324779,2	MCF-7	breast:
5	chr9:86230729..86232939-chr9:86244046..86245933,2	K562	blood:
6	chr9:86210303..86212582-chr9:86243491..86245294,2	MCF-7	breast:
7	chr9:86243566..86245560-chr9:86258572..86260267,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000199483	Chromatin interaction
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10115799	0.92[CHB][hapmap]
rs10119344	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10125432	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1035274	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1044175	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10746718	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10746719	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10746720	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10746721	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10780621	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10868040	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10868044	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10868045	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1333863	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1333865	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1413293	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1572135	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1889260	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058912	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2542776	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2780969	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2780972	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2780977	0.84[EUR][1000 genomes]
rs2780978	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2780979	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780981	0.81[EUR][1000 genomes]
rs2780982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780995	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2781000	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2781003	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2811899	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2811900	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811902	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811903	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811909	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2811912	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2811919	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2811923	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2811926	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2811927	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2811928	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2811929	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2811930	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2811931	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3750410	0.86[CHB][hapmap]
rs4146741	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4242623	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6559737	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7018643	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7023082	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7039019	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7865296	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7871055	0.86[CHB][hapmap]
rs7874980	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs961807	0.92[CHB][hapmap];1.00[JPT][hapmap]

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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv516587	chr9:86226119-86255765	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv973848	chr9:86241130-86260149	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86238600-86265000	Weak transcription	Ovary	ovary
2	chr9:86238800-86246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:86238800-86246000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:86238800-86254600	Weak transcription	Left Ventricle	heart
5	chr9:86238800-86260600	Weak transcription	Right Ventricle	heart
6	chr9:86238800-86264600	Weak transcription	Psoas Muscle	Psoas
7	chr9:86239000-86245200	Weak transcription	Fetal Kidney	kidney
8	chr9:86239000-86245400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:86239000-86250000	Weak transcription	HSMMtube	muscle
10	chr9:86239000-86264800	Weak transcription	HMEC	breast
11	chr9:86239000-86265200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:86239200-86245800	Weak transcription	Brain Germinal Matrix	brain
13	chr9:86239200-86261000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:86239400-86245400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:86239400-86245800	Weak transcription	Fetal Heart	heart
16	chr9:86239400-86245800	Weak transcription	Fetal Lung	lung
17	chr9:86239400-86248000	Weak transcription	NHDF-Ad	bronchial
18	chr9:86239400-86254400	Weak transcription	Brain Anterior Caudate	brain
19	chr9:86239400-86254400	Weak transcription	Brain Substantia Nigra	brain
20	chr9:86239400-86266200	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:86239400-86266400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:86239600-86245600	Weak transcription	Brain Angular Gyrus	brain
23	chr9:86239600-86245600	Weak transcription	Fetal Brain Female	brain
24	chr9:86239600-86260800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:86239600-86260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:86239600-86265000	Weak transcription	HUVEC	blood vessel
27	chr9:86239600-86266600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:86239600-86272200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:86239800-86266800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr9:86240000-86246000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:86240200-86265000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr9:86240400-86254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr9:86240600-86245800	Weak transcription	K562	blood
34	chr9:86240800-86245000	Strong transcription	Fetal Muscle Leg	muscle
35	chr9:86241000-86245000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:86241200-86245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:86241400-86245000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:86241400-86245000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:86241400-86245000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:86241400-86245200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr9:86241600-86245000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:86241600-86245000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:86241600-86245000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:86241600-86245000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:86241600-86245000	Strong transcription	Fetal Stomach	stomach
46	chr9:86241600-86245000	Genic enhancers	Thymus	Thymus
47	chr9:86241600-86245200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:86242200-86256600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:86242400-86246000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:86242400-86253800	Weak transcription	Brain Inferior Temporal Lobe	brain

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