Variant report

Variant	rs177042
Chromosome Location	chr9:86599756-86599757
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86534483..86536598-chr9:86598501..86601321,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10124390	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125673	0.88[ASN][1000 genomes]
rs10780639	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10780640	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10868077	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004439	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12006540	0.80[AMR][1000 genomes]
rs12551039	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1572030	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296891	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296892	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877814	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877815	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5018100	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6559753	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6559754	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6559756	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7020841	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7021189	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045008	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7864367	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7875011	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875242	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796000	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796001	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796002	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
2	chr9:86596600-86601800	Weak transcription	Pancreas	Pancrea
3	chr9:86596600-86603200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:86596600-86610600	Weak transcription	Esophagus	oesophagus
5	chr9:86596600-86613400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:86596600-86613800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:86596600-86616000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:86596600-86617000	Weak transcription	Lung	lung
9	chr9:86596600-86618200	Weak transcription	Ovary	ovary
10	chr9:86596600-86619600	Weak transcription	Gastric	stomach
11	chr9:86596800-86601200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr9:86596800-86601200	Weak transcription	Liver	Liver
13	chr9:86596800-86601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:86596800-86601800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:86596800-86601800	Weak transcription	Left Ventricle	heart
16	chr9:86596800-86601800	Weak transcription	HSMM	muscle
17	chr9:86596800-86602000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr9:86596800-86603200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:86596800-86603200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:86596800-86603200	Weak transcription	Fetal Thymus	thymus
21	chr9:86596800-86605400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:86596800-86606600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:86596800-86613200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:86596800-86614400	Weak transcription	HSMMtube	muscle
25	chr9:86596800-86616000	Weak transcription	Brain Hippocampus Middle	brain
26	chr9:86596800-86616200	Weak transcription	Brain Angular Gyrus	brain
27	chr9:86596800-86616200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:86596800-86619600	Weak transcription	Small Intestine	intestine
29	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:86597000-86600400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:86597000-86600600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr9:86597000-86601000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr9:86597000-86601200	Weak transcription	Osteobl	bone
35	chr9:86597000-86601400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr9:86597000-86602000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:86597000-86602800	Weak transcription	Fetal Intestine Small	intestine
38	chr9:86597000-86603200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:86597000-86603200	Weak transcription	Fetal Muscle Leg	muscle
40	chr9:86597000-86603400	Weak transcription	Fetal Intestine Large	intestine
41	chr9:86597000-86603600	Weak transcription	Thymus	Thymus
42	chr9:86597000-86609600	Weak transcription	Primary T cells from cord blood	blood
43	chr9:86597000-86614200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:86597000-86616000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:86597000-86616000	Weak transcription	Fetal Lung	lung
46	chr9:86597000-86617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:86597000-86621200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:86597000-86621600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:86597200-86600400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr9:86597200-86601000	Weak transcription	Primary hematopoietic stem cells	blood

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