Variant report

Variant	rs10259741
Chromosome Location	chr7:111907510-111907511
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	chr7:111900844..111903692-chr7:111905399..111908941,4	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10226284	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10238141	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10247876	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272126	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10272188	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10953708	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953709	0.87[EUR][1000 genomes]
rs10953710	0.87[EUR][1000 genomes]
rs11760599	0.93[EUR][1000 genomes]
rs11761807	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11762497	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11763356	0.85[ASN][1000 genomes]
rs11763768	0.82[ASN][1000 genomes]
rs11767115	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11768608	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11768793	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11768891	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11769219	0.85[ASN][1000 genomes]
rs11770767	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11773393	0.81[ASN][1000 genomes]
rs12666261	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12666328	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12668065	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12673830	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16873374	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17159389	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17159446	0.82[EUR][1000 genomes]
rs2301725	0.81[EUR][1000 genomes]
rs3807884	0.93[ASN][1000 genomes]
rs3823515	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4730516	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730517	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55915049	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56675883	0.87[EUR][1000 genomes]
rs56969420	0.82[ASN][1000 genomes]
rs60445595	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6949164	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6955231	0.82[ASN][1000 genomes]
rs7781245	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7792130	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7795336	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9641480	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9641481	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531435	chr7:111333900-111926292	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv491934	chr7:111333900-111975504	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:111893200-111926000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:111896000-111913000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:111896800-111922200	Weak transcription	Pancreas	Pancrea
4	chr7:111897600-111908000	Weak transcription	HepG2	liver
5	chr7:111903400-111949200	Weak transcription	Fetal Intestine Small	intestine
6	chr7:111903800-111908600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:111903800-111913000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:111903800-111916000	Weak transcription	Small Intestine	intestine
9	chr7:111903800-111917000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:111903800-111926000	Weak transcription	Psoas Muscle	Psoas
11	chr7:111904000-111907600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:111904000-111907600	Weak transcription	Brain Angular Gyrus	brain
13	chr7:111904000-111907600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:111904000-111907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:111904200-111907600	Weak transcription	Brain Substantia Nigra	brain
16	chr7:111904200-111908200	Weak transcription	Fetal Lung	lung
17	chr7:111905000-111908200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr7:111905200-111907600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:111905400-111907800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr7:111905400-111908200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:111905400-111926000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:111905600-111907800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:111906000-111907800	Enhancers	HMEC	breast
24	chr7:111906200-111907600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:111906200-111907600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:111906200-111908000	Enhancers	Brain Anterior Caudate	brain
27	chr7:111906400-111907800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:111906600-111913200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:111906600-111913200	Weak transcription	Ovary	ovary
30	chr7:111906600-111915200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:111907000-111907600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:111907000-111908000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:111907000-111908400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:111907200-111907800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr7:111907200-111913200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:111907200-111915600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr7:111907200-111922400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:111907400-111908000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr7:111907400-111908200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr7:111907400-111908200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr7:111907400-111908800	Enhancers	Brain Hippocampus Middle	brain
42	chr7:111907400-111928400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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