Variant report

Variant	rs2373688
Chromosome Location	chr2:39949194-39949195
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	chr2:39947562..39949942-chr2:39951658..39954303,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10206408	0.88[AMR][1000 genomes]
rs11124691	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12617624	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12623462	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12623545	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12624217	0.80[AMR][1000 genomes]
rs13401182	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13425906	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1978327	0.81[EUR][1000 genomes]
rs1986876	0.81[ASN][1000 genomes]
rs2041735	0.83[ASN][1000 genomes]
rs2058620	0.83[ASN][1000 genomes]
rs2110656	0.81[ASN][1000 genomes]
rs2160198	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2215958	0.85[EUR][1000 genomes]
rs2540226	0.86[ASN][1000 genomes]
rs2540227	0.84[ASN][1000 genomes]
rs2540229	0.84[EUR][1000 genomes]
rs2716704	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2716727	0.89[ASN][1000 genomes]
rs2716729	0.86[ASN][1000 genomes]
rs2716730	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3902124	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4365444	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4644998	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670955	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4670956	0.81[ASN][1000 genomes]
rs4670957	0.88[AMR][1000 genomes]
rs4670958	0.88[AMR][1000 genomes]
rs4670959	0.80[AMR][1000 genomes]
rs6719179	0.83[AMR][1000 genomes]
rs6731026	0.81[ASN][1000 genomes]
rs6731450	0.81[ASN][1000 genomes]
rs6750252	0.81[ASN][1000 genomes]
rs7565954	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7581406	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7591296	0.88[ASN][1000 genomes]
rs7591347	0.88[ASN][1000 genomes]
rs917960	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs917962	0.82[ASN][1000 genomes]
rs917963	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs962262	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
2	chr2:39925200-39950000	Weak transcription	Left Ventricle	heart
3	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:39936600-39950600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:39938000-39957600	Weak transcription	Fetal Brain Female	brain
6	chr2:39938200-39950600	Weak transcription	HSMMtube	muscle
7	chr2:39938400-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:39940800-39950800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:39943200-39956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
12	chr2:39945200-39954400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:39946400-39950600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:39946600-39949800	Weak transcription	Psoas Muscle	Psoas
15	chr2:39946600-39951200	Weak transcription	Aorta	Aorta
16	chr2:39946800-39950000	Weak transcription	NH-A	brain
17	chr2:39946800-39950600	Weak transcription	Osteobl	bone
18	chr2:39946800-39959600	Weak transcription	Brain Germinal Matrix	brain
19	chr2:39947800-39950200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:39947800-39959800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:39948000-39949800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:39948200-39961200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:39948400-39950800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:39948600-39950800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:39948600-39950800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:39948600-39950800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:39948800-39952400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:39948800-39959600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:39949000-39950800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:39949000-39950800	Enhancers	Fetal Heart	heart
31	chr2:39949000-39951000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:39949000-39951000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:39949000-39952400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:39949000-39960400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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