Variant report

Variant	rs10280009
Chromosome Location	chr7:104621217-104621218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:104619886..104621956-chr7:104705400..104707760,2	K562	blood:
2	chr7:104607959..104610771-chr7:104619164..104621413,2	MCF-7	breast:
3	chr7:104615466..104619404-chr7:104620250..104622785,4	MCF-7	breast:
4	chr7:104620361..104623335-chr7:104771207..104773173,3	K562	blood:
5	chr7:104598820..104600629-chr7:104619453..104622202,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1013016	0.91[AMR][1000 genomes]
rs10224526	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10231782	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10231975	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10242713	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10244764	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10245589	0.84[EUR][1000 genomes]
rs10245676	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10245796	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10249746	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10249965	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10253962	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10260346	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10261472	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10261573	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10264273	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10268866	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10274607	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10276583	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10279486	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10279602	0.83[EUR][1000 genomes]
rs10280752	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10808139	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10808140	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10953464	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10953467	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11971732	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11973516	0.82[AMR][1000 genomes]
rs11976329	0.83[EUR][1000 genomes]
rs11981399	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12171585	0.80[AMR][1000 genomes]
rs12531424	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12532062	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12532456	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12534140	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12540007	0.83[EUR][1000 genomes]
rs12671368	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12705297	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12705299	0.82[EUR][1000 genomes]
rs13230660	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967301	0.83[AMR][1000 genomes]
rs2011258	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2058711	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2216107	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2237602	0.83[EUR][1000 genomes]
rs2237605	0.83[EUR][1000 genomes]
rs2240453	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2240454	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2240455	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2240457	0.83[EUR][1000 genomes]
rs2285532	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299299	0.82[EUR][1000 genomes]
rs28489493	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2891761	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3173872	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213676	0.83[EUR][1000 genomes]
rs3213741	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34202980	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34558707	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35780942	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3735377	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3815256	0.85[AMR][1000 genomes]
rs4730065	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4730067	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4730068	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4730069	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6466043	0.88[AMR][1000 genomes]
rs6466045	0.85[AMR][1000 genomes]
rs67739707	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6952534	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6972229	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71562633	0.82[EUR][1000 genomes]
rs740297	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs740298	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs740300	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs757958	0.80[AMR][1000 genomes]
rs7785197	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7800233	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7805792	0.84[AMR][1000 genomes]
rs7810119	0.83[EUR][1000 genomes]
rs7811349	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs875567	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs875568	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs916704	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs960437	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9641340	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9641341	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs999895	0.83[AMR][1000 genomes];0.84[EUR][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	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	nsv516060	chr7:104618318-104622402	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv526422	chr7:104618318-104632980	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104587200-104623600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:104598000-104621600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr7:104598200-104621400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr7:104598200-104623000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:104601800-104622800	Weak transcription	Thymus	Thymus
6	chr7:104606600-104622000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:104608400-104623000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:104612800-104621400	Weak transcription	Liver	Liver
9	chr7:104614400-104621400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:104615200-104622000	Weak transcription	Fetal Heart	heart
11	chr7:104616200-104622800	Enhancers	Stomach Smooth Muscle	stomach
12	chr7:104616200-104623400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr7:104616400-104622800	Enhancers	NHDF-Ad	bronchial
14	chr7:104616800-104621400	Enhancers	Colon Smooth Muscle	Colon
15	chr7:104616800-104623400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr7:104616800-104623400	Enhancers	Adipose Nuclei	Adipose
17	chr7:104617200-104622800	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr7:104617200-104623000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr7:104617400-104623200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:104617600-104623200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:104617600-104623400	Weak transcription	Lung	lung
22	chr7:104617600-104623400	Enhancers	Osteobl	bone
23	chr7:104618000-104623200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr7:104618200-104622200	Weak transcription	Fetal Brain Male	brain
25	chr7:104618200-104623400	Weak transcription	Aorta	Aorta
26	chr7:104618400-104622200	Weak transcription	Fetal Brain Female	brain
27	chr7:104618600-104622600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:104618600-104624200	Weak transcription	Gastric	stomach
29	chr7:104618800-104621400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:104618800-104622000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr7:104619000-104621800	Enhancers	HMEC	breast
32	chr7:104619000-104621800	Enhancers	NH-A	brain
33	chr7:104619000-104623600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:104619200-104622200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:104619400-104623600	Enhancers	HUVEC	blood vessel
36	chr7:104619600-104621400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:104619600-104621400	Genic enhancers	HSMM	muscle
38	chr7:104619600-104623400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:104619800-104621600	Weak transcription	Dnd41	blood
40	chr7:104619800-104622000	Weak transcription	Fetal Intestine Large	intestine
41	chr7:104619800-104622600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr7:104619800-104622800	Weak transcription	Fetal Intestine Small	intestine
43	chr7:104619800-104623000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:104620000-104621800	Weak transcription	K562	blood
45	chr7:104620000-104622400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr7:104620000-104622800	Weak transcription	Small Intestine	intestine
47	chr7:104620000-104623000	Weak transcription	Fetal Lung	lung
48	chr7:104620000-104623400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr7:104620000-104623400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr7:104620000-104623600	Weak transcription	Ovary	ovary

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