Variant report

Variant	rs10820804
Chromosome Location	chr9:108216132-108216133
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	chr9:108210042..108212284-chr9:108213571..108216466,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106701	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1048215	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10491809	1.00[CEU][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10816281	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10816283	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816285	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816286	0.84[EUR][1000 genomes]
rs10816287	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816288	0.85[EUR][1000 genomes]
rs10816289	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820811	0.91[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10820814	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10820815	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978169	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10978172	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978176	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978177	0.89[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978179	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10991659	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10991673	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10991677	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10991679	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11562356	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12336250	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12336844	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12337780	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12345599	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12352975	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1327352	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1327355	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1887367	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296750	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297023	0.89[ASN][1000 genomes]
rs2417625	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28542455	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28851907	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3750500	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3793639	0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3818598	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55798036	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7023302	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7023520	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7033138	0.81[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7033165	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7034149	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7037104	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7037141	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7037218	0.91[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7038407	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7045862	0.83[YRI][hapmap]
rs7047791	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72744263	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72744264	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7852541	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7854411	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7856617	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7857186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs997319	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108211200-108219800	Weak transcription	Lung	lung
3	chr9:108211200-108220000	Weak transcription	Left Ventricle	heart
4	chr9:108211200-108220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:108211200-108220400	Weak transcription	Primary B cells from cord blood	blood
6	chr9:108211200-108220600	Weak transcription	Ovary	ovary
7	chr9:108211400-108220000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:108211400-108220000	Weak transcription	Right Ventricle	heart
9	chr9:108211400-108222000	Weak transcription	Stomach Mucosa	stomach
10	chr9:108211600-108219600	Weak transcription	Brain Substantia Nigra	brain
11	chr9:108211600-108220000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:108211800-108219600	Weak transcription	Brain Angular Gyrus	brain
13	chr9:108211800-108219800	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:108211800-108220000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:108211800-108227000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:108212200-108216800	Weak transcription	Psoas Muscle	Psoas
17	chr9:108212200-108218200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:108212200-108219600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:108212200-108219600	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:108212200-108219800	Weak transcription	Brain Anterior Caudate	brain
21	chr9:108212200-108220000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:108212200-108220000	Weak transcription	Fetal Intestine Small	intestine
23	chr9:108212200-108220400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr9:108212200-108220600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:108212200-108234800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:108212400-108219600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:108212400-108219800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:108212600-108216600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:108212600-108220000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:108212600-108220000	Weak transcription	NHEK	skin
31	chr9:108212800-108216200	Enhancers	HepG2	liver
32	chr9:108212800-108218200	Weak transcription	Fetal Heart	heart
33	chr9:108212800-108218800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:108212800-108219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:108212800-108220200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:108212800-108220200	Weak transcription	Hela-S3	cervix
37	chr9:108212800-108226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:108213200-108217800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:108213600-108219800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:108214000-108219200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:108214000-108219600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:108214000-108220000	Weak transcription	A549	lung
43	chr9:108214200-108218200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:108214200-108220400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr9:108214400-108217400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:108214400-108217800	Weak transcription	NHDF-Ad	bronchial
47	chr9:108214400-108219200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr9:108214400-108219400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:108214400-108219800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:108214400-108220000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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