Variant report

Variant	rs28841370
Chromosome Location	chr2:48575662-48575663
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48568770..48570498-chr2:48574091..48575734,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10153773	0.94[ASN][1000 genomes]
rs10174717	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10180295	0.88[ASN][1000 genomes]
rs10186237	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10193072	0.88[ASN][1000 genomes]
rs10199431	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10208124	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11676168	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11682044	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11682931	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11685861	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11690690	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12616792	0.82[ASN][1000 genomes]
rs12713008	0.82[ASN][1000 genomes]
rs13003076	0.87[ASN][1000 genomes]
rs13383364	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13385535	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13386751	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13387171	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13388291	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13392004	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13426834	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13432998	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2471405	0.83[ASN][1000 genomes]
rs28806843	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4290706	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4344965	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4411759	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4547573	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4641990	0.91[ASN][1000 genomes]
rs56163539	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56352447	0.92[ASN][1000 genomes]
rs57668696	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58660534	0.99[ASN][1000 genomes]
rs59264464	0.88[ASN][1000 genomes]
rs59412192	0.88[ASN][1000 genomes]
rs59761994	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60677957	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136987	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62137001	0.99[ASN][1000 genomes]
rs62137002	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62137003	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62137005	0.99[ASN][1000 genomes]
rs62137006	1.00[ASN][1000 genomes]
rs62137007	1.00[ASN][1000 genomes]
rs62137008	0.97[ASN][1000 genomes]
rs62137009	0.97[ASN][1000 genomes]
rs62137015	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62138801	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545027	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545028	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545029	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6545030	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545034	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545035	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545036	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6712029	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743757	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6745580	0.94[AFR][1000 genomes]
rs6749773	0.87[AMR][1000 genomes]
rs6757206	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72818493	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72820405	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72887649	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7340322	0.83[ASN][1000 genomes]
rs7562069	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7562816	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7568960	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7573316	0.82[AFR][1000 genomes]
rs7574125	0.92[ASN][1000 genomes]
rs7576964	0.82[AFR][1000 genomes]
rs7577237	0.81[AFR][1000 genomes]
rs7579932	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7600794	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7606104	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9309152	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:48570800-48577400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:48571000-48577000	Weak transcription	Spleen	Spleen
4	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
5	chr2:48571600-48580000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:48572200-48597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:48572400-48580000	Weak transcription	Stomach Mucosa	stomach
8	chr2:48573000-48576200	ZNF genes & repeats	Dnd41	blood
9	chr2:48573000-48578000	ZNF genes & repeats	GM12878-XiMat	blood
10	chr2:48573200-48576400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
11	chr2:48573200-48576400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr2:48573200-48577600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:48573200-48577800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr2:48573200-48578400	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr2:48573200-48578800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:48573200-48579400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr2:48573400-48576000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
18	chr2:48573400-48576000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
19	chr2:48573400-48576200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr2:48573400-48576200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:48573400-48576200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:48573400-48576200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
23	chr2:48573400-48576200	ZNF genes & repeats	K562	blood
24	chr2:48573400-48576200	ZNF genes & repeats	NHEK	skin
25	chr2:48573400-48576400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr2:48573400-48576400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr2:48573400-48576600	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr2:48573400-48577000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
29	chr2:48573400-48578000	ZNF genes & repeats	Fetal Intestine Large	intestine
30	chr2:48573400-48578000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr2:48573400-48578400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr2:48573400-48578800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr2:48573400-48579200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:48573400-48579200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:48573400-48583200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:48573600-48576200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
37	chr2:48573600-48578600	Weak transcription	Pancreas	Pancrea
38	chr2:48573600-48579000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:48573600-48579200	ZNF genes & repeats	A549	lung
40	chr2:48573600-48579400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:48573600-48579400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr2:48573600-48604000	Weak transcription	Ovary	ovary
43	chr2:48573800-48575800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:48573800-48575800	Weak transcription	Brain Angular Gyrus	brain
45	chr2:48573800-48576000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:48573800-48576000	Weak transcription	Left Ventricle	heart
47	chr2:48573800-48576200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
48	chr2:48573800-48576200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:48573800-48576200	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
50	chr2:48573800-48577000	ZNF genes & repeats	Fetal Lung	lung

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