Variant report

Variant	rs62137009
Chromosome Location	chr2:48574164-48574165
allele	C/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: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10153773	0.91[ASN][1000 genomes]
rs10174717	0.89[ASN][1000 genomes]
rs10180295	0.86[ASN][1000 genomes]
rs10186237	0.86[ASN][1000 genomes]
rs10193072	0.86[ASN][1000 genomes]
rs10199431	0.93[ASN][1000 genomes]
rs10208124	0.85[ASN][1000 genomes]
rs11676168	0.89[ASN][1000 genomes]
rs11682044	0.87[ASN][1000 genomes]
rs11690748	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11690845	0.85[AFR][1000 genomes]
rs13003076	0.84[ASN][1000 genomes]
rs13383364	0.85[ASN][1000 genomes]
rs13385535	0.89[ASN][1000 genomes]
rs13386751	0.83[ASN][1000 genomes]
rs13387171	0.86[ASN][1000 genomes]
rs13388291	0.85[ASN][1000 genomes]
rs13426834	0.83[ASN][1000 genomes]
rs13432998	0.84[ASN][1000 genomes]
rs17037289	0.84[AFR][1000 genomes]
rs2471405	0.80[ASN][1000 genomes]
rs28806843	0.85[ASN][1000 genomes]
rs28841370	0.97[ASN][1000 genomes]
rs4290706	0.87[ASN][1000 genomes]
rs4411759	0.90[ASN][1000 genomes]
rs4547573	0.83[ASN][1000 genomes]
rs4641990	0.89[ASN][1000 genomes]
rs56352447	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57668696	0.94[ASN][1000 genomes]
rs57893565	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58012056	0.84[AFR][1000 genomes]
rs58660534	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59264464	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59412192	0.85[ASN][1000 genomes]
rs59761994	0.96[ASN][1000 genomes]
rs60677957	0.82[ASN][1000 genomes]
rs62136987	0.97[ASN][1000 genomes]
rs62137001	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62137002	0.96[ASN][1000 genomes]
rs62137003	0.96[ASN][1000 genomes]
rs62137005	0.96[ASN][1000 genomes]
rs62137006	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137007	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137008	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62138801	0.86[ASN][1000 genomes]
rs6545027	0.83[ASN][1000 genomes]
rs6545028	0.83[ASN][1000 genomes]
rs6545030	0.91[ASN][1000 genomes]
rs6545034	0.94[ASN][1000 genomes]
rs6545035	0.94[ASN][1000 genomes]
rs6712029	0.91[ASN][1000 genomes]
rs6757206	0.83[ASN][1000 genomes]
rs72818493	0.87[ASN][1000 genomes]
rs72820405	0.96[ASN][1000 genomes]
rs72820427	0.85[AFR][1000 genomes]
rs72887649	0.87[ASN][1000 genomes]
rs7340322	0.80[ASN][1000 genomes]
rs7568960	0.82[ASN][1000 genomes]
rs7574125	0.89[ASN][1000 genomes]
rs9309152	0.93[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:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48553400-48574400	Weak transcription	Lung	lung
2	chr2:48564800-48574400	Weak transcription	Fetal Stomach	stomach
3	chr2:48569000-48574400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:48570800-48575600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:48570800-48577400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:48571000-48574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:48571000-48574400	Weak transcription	Small Intestine	intestine
9	chr2:48571000-48577000	Weak transcription	Spleen	Spleen
10	chr2:48571200-48574800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
12	chr2:48571600-48580000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:48571800-48574200	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:48571800-48574400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:48571800-48574400	Enhancers	Adipose Nuclei	Adipose
16	chr2:48572000-48574400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:48572200-48597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:48572400-48580000	Weak transcription	Stomach Mucosa	stomach
19	chr2:48572800-48574400	Enhancers	Liver	Liver
20	chr2:48573000-48574200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:48573000-48576200	ZNF genes & repeats	Dnd41	blood
22	chr2:48573000-48578000	ZNF genes & repeats	GM12878-XiMat	blood
23	chr2:48573200-48576400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr2:48573200-48576400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
25	chr2:48573200-48577600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:48573200-48577800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr2:48573200-48578400	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr2:48573200-48578800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:48573200-48579400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr2:48573400-48574600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr2:48573400-48574600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:48573400-48574800	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr2:48573400-48574800	ZNF genes & repeats	Fetal Thymus	thymus
34	chr2:48573400-48574800	ZNF genes & repeats	Thymus	Thymus
35	chr2:48573400-48575200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
36	chr2:48573400-48576000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
37	chr2:48573400-48576000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr2:48573400-48576200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
39	chr2:48573400-48576200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:48573400-48576200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:48573400-48576200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
42	chr2:48573400-48576200	ZNF genes & repeats	K562	blood
43	chr2:48573400-48576200	ZNF genes & repeats	NHEK	skin
44	chr2:48573400-48576400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr2:48573400-48576400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr2:48573400-48576600	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr2:48573400-48577000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
48	chr2:48573400-48578000	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr2:48573400-48578000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr2:48573400-48578400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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