Variant report

Variant	rs2238045
Chromosome Location	chr12:2299823-2299824
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	chr12:2299454..2301244-chr12:2302149..2304178,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1016388	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459125	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744559	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774030	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10774032	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774033	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10848627	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848628	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848629	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848631	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848632	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848633	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848634	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10848635	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848636	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848637	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11062145	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11062146	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11062147	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11062148	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11062156	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11614764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423277	0.85[ASN][1000 genomes]
rs1860056	0.85[ASN][1000 genomes]
rs2098013	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238046	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238047	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2238048	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238049	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238050	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238052	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238053	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238054	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238056	0.84[ASN][1000 genomes]
rs2239018	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239019	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239020	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239021	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239022	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239023	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239024	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239025	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239026	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239027	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239030	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239033	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283287	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283288	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283291	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34382810	0.88[ASN][1000 genomes]
rs34640767	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794297	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4765668	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4765669	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765670	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765902	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6489353	0.95[ASN][1000 genomes]
rs7133502	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308351	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758171	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs758172	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs758173	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs758174	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7957545	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1035885	chr12:2077660-2310157	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv541350	chr12:2077660-2310157	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1038722	chr12:2085035-2308205	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv541351	chr12:2085035-2308205	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv898604	chr12:2236842-2317523	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv898605	chr12:2252924-2327944	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3401913	chr12:2298691-2303189	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2289600-2303200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:2289800-2300400	Weak transcription	Aorta	Aorta
3	chr12:2290000-2300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:2293600-2301400	Weak transcription	Brain Germinal Matrix	brain
5	chr12:2293800-2300600	Weak transcription	Fetal Heart	heart
6	chr12:2293800-2301000	Weak transcription	Brain Angular Gyrus	brain
7	chr12:2293800-2303000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:2294000-2300400	Weak transcription	NHLF	lung
9	chr12:2294000-2300800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:2294000-2300800	Weak transcription	Fetal Lung	lung
11	chr12:2294000-2300800	Weak transcription	NHDF-Ad	bronchial
12	chr12:2294000-2303800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:2294000-2325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:2294200-2300000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:2294200-2303600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:2294400-2300200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:2294400-2300800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:2294400-2303200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:2294600-2300400	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:2294600-2300400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:2294600-2302000	Weak transcription	Spleen	Spleen
22	chr12:2295600-2303800	Weak transcription	Fetal Stomach	stomach
23	chr12:2295800-2302400	Weak transcription	Osteobl	bone
24	chr12:2296200-2300600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:2298400-2300400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr12:2298400-2300800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr12:2298400-2301600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:2298400-2301800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:2298400-2302200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:2298400-2302200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:2298400-2302400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr12:2298400-2304800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr12:2298800-2301800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:2298800-2301800	Weak transcription	Right Ventricle	heart
35	chr12:2298800-2302200	Weak transcription	Left Ventricle	heart
36	chr12:2299200-2306200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:2299800-2300600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:2299800-2300800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:2299800-2300800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:2299800-2302800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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