Variant report

Variant	rs62156488
Chromosome Location	chr2:98549007-98549008
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	chr2:98543155..98545618-chr2:98548793..98550382,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs55853292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55887737	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58415781	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58576615	0.82[AFR][1000 genomes]
rs58690282	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59049638	0.83[EUR][1000 genomes]
rs59444417	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59635122	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs59752876	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60567628	0.86[AFR][1000 genomes]
rs61363543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62154513	0.85[AMR][1000 genomes]
rs62154516	0.85[AFR][1000 genomes]
rs62154549	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62154552	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154553	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154556	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154558	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62156480	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62156482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62156507	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62156508	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156514	0.93[EUR][1000 genomes]
rs62156519	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62156522	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62156523	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62156524	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62156525	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62156526	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62156527	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62156530	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62157630	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs62158265	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62158266	0.88[EUR][1000 genomes]
rs62158268	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62158269	0.83[EUR][1000 genomes]
rs62158270	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62158272	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73960406	0.86[AFR][1000 genomes]
rs73960407	0.86[AFR][1000 genomes]
rs73960426	0.86[AFR][1000 genomes]
rs73960430	0.89[AFR][1000 genomes]
rs73960433	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73960435	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7420897	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7575922	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7600204	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7606272	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr2:98504600-98552200	Weak transcription	NHLF	lung
2	chr2:98520200-98552200	Weak transcription	Brain Angular Gyrus	brain
3	chr2:98520600-98550600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:98524600-98552600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:98524800-98552200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:98525000-98551600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:98528600-98550600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:98529000-98552200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:98531000-98552400	Weak transcription	Right Atrium	heart
10	chr2:98531200-98552200	Weak transcription	Fetal Thymus	thymus
11	chr2:98533800-98552000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:98534200-98551600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:98538800-98552400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:98539000-98551600	Weak transcription	A549	lung
15	chr2:98541200-98552400	Weak transcription	Esophagus	oesophagus
16	chr2:98541400-98552200	Weak transcription	NHEK	skin
17	chr2:98541600-98550400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:98541600-98552400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:98541600-98552400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:98541600-98552400	Weak transcription	Aorta	Aorta
21	chr2:98541600-98552400	Weak transcription	Lung	lung
22	chr2:98541800-98552400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:98542000-98552000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:98542000-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:98542000-98552200	Weak transcription	Right Ventricle	heart
26	chr2:98542000-98552200	Weak transcription	HepG2	liver
27	chr2:98542000-98552400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:98542000-98552400	Weak transcription	Left Ventricle	heart
29	chr2:98542000-98552400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:98542000-98552400	Weak transcription	Thymus	Thymus
31	chr2:98542000-98552800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:98542200-98550000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:98542200-98550200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:98542200-98550400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:98542200-98551000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:98542200-98551600	Weak transcription	Dnd41	blood
37	chr2:98542200-98551800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:98542200-98551800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:98542200-98552000	Weak transcription	Osteobl	bone
40	chr2:98542200-98552200	Weak transcription	Fetal Brain Female	brain
41	chr2:98542200-98552200	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:98542200-98552400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:98542200-98552400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr2:98542200-98552400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:98542200-98552400	Weak transcription	Placenta	Placenta
46	chr2:98542600-98552200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:98542600-98552400	Weak transcription	Fetal Stomach	stomach
48	chr2:98542800-98550600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:98543000-98549800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:98543000-98552000	Weak transcription	HMEC	breast

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