Variant report

Variant	rs1980725
Chromosome Location	chr9:110058965-110058966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110056937..110059349-chr9:110068583..110071542,3	MCF-7	breast:
2	chr9:110058012..110060076-chr9:110062055..110063823,2	MCF-7	breast:
3	chr9:110005542..110008121-chr9:110058915..110061761,2	MCF-7	breast:
4	chr9:110043397..110048376-chr9:110058875..110065071,10	K562	blood:
5	chr9:110050921..110052628-chr9:110056459..110059114,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10481632	0.80[AFR][1000 genomes]
rs10521083	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10732368	0.94[ASN][1000 genomes]
rs10739234	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739236	0.80[AFR][1000 genomes]
rs10739237	0.85[ASN][1000 genomes]
rs10739238	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759222	0.94[ASN][1000 genomes]
rs10759223	0.94[ASN][1000 genomes]
rs10759225	0.81[ASN][1000 genomes]
rs10759226	0.91[ASN][1000 genomes]
rs10816483	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10816485	0.80[AFR][1000 genomes]
rs10816486	0.94[ASN][1000 genomes]
rs10816487	0.93[ASN][1000 genomes]
rs10816490	0.80[AFR][1000 genomes]
rs10816492	0.81[ASN][1000 genomes]
rs10816493	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10978791	0.80[AFR][1000 genomes]
rs10978798	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1323808	0.91[ASN][1000 genomes]
rs1323809	0.81[ASN][1000 genomes]
rs1535765	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805332	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805334	0.96[ASN][1000 genomes]
rs1805335	0.91[ASN][1000 genomes]
rs1886134	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1969798	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2147071	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147072	0.94[ASN][1000 genomes]
rs2417783	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2417784	0.80[AFR][1000 genomes]
rs2417785	0.91[ASN][1000 genomes]
rs28534368	0.80[AFR][1000 genomes]
rs3818367	0.96[ASN][1000 genomes]
rs4278207	1.00[ASN][1000 genomes]
rs4625087	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978404	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4978406	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4978844	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4978849	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61701375	0.80[AFR][1000 genomes]
rs7019341	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7025563	0.94[ASN][1000 genomes]
rs7029997	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030169	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7030555	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7030631	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031906	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7035611	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7035725	0.86[ASN][1000 genomes]
rs7038737	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039041	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040217	0.81[EUR][1000 genomes]
rs7041137	0.81[EUR][1000 genomes]
rs7041497	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7043962	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7046950	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7856112	0.91[ASN][1000 genomes]
rs7856227	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7859769	0.91[ASN][1000 genomes]
rs817836	0.80[AFR][1000 genomes]
rs817838	0.81[EUR][1000 genomes]
rs817839	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs817840	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs817841	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs817843	0.81[EUR][1000 genomes]
rs817844	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs817845	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs942292	0.91[ASN][1000 genomes]
rs942293	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9632893	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110047600-110067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:110048800-110059200	Enhancers	HepG2	liver
3	chr9:110048800-110061000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr9:110048800-110067800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:110048800-110069600	Weak transcription	Fetal Brain Male	brain
6	chr9:110049000-110061200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:110049000-110061400	Weak transcription	NH-A	brain
8	chr9:110049000-110063000	Enhancers	Liver	Liver
9	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:110049200-110059200	Weak transcription	Fetal Intestine Small	intestine
12	chr9:110049200-110067000	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:110049400-110067800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:110050200-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:110051200-110066000	Weak transcription	Fetal Intestine Large	intestine
16	chr9:110051200-110067000	Weak transcription	Thymus	Thymus
17	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:110052000-110066800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:110052200-110061200	Weak transcription	Dnd41	blood
20	chr9:110052600-110063200	Weak transcription	Placenta	Placenta
21	chr9:110052600-110067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:110052600-110067000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:110052600-110068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:110052600-110068600	Weak transcription	Brain Germinal Matrix	brain
25	chr9:110052600-110068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:110052600-110069200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr9:110052800-110061200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:110052800-110066000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:110053400-110068600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:110053600-110061200	Weak transcription	Hela-S3	cervix
31	chr9:110053600-110063200	Weak transcription	Fetal Thymus	thymus
32	chr9:110053600-110063400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:110055600-110061200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:110055600-110063000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr9:110055600-110067600	Weak transcription	HSMMtube	muscle
36	chr9:110055600-110068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:110055800-110061200	Weak transcription	HMEC	breast
38	chr9:110055800-110068600	Weak transcription	Fetal Brain Female	brain
39	chr9:110055800-110068600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:110056000-110061200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:110056000-110062600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr9:110056400-110061200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:110056400-110061200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr9:110056400-110061600	Weak transcription	HSMM	muscle
45	chr9:110056400-110063400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:110056800-110061200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:110056800-110061600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:110056800-110062400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr9:110056800-110065800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:110056800-110068600	Weak transcription	Lung	lung

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