Variant report

Variant	rs152208
Chromosome Location	chr5:61715040-61715041
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	chr5:61708374..61709879-chr5:61712891..61715060,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086200	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10058044	0.85[ASN][1000 genomes]
rs10060589	0.85[ASN][1000 genomes]
rs10065749	0.85[ASN][1000 genomes]
rs10069745	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10461472	0.81[EUR][1000 genomes]
rs10939937	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12515967	0.80[EUR][1000 genomes]
rs1301063	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1309156	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13174978	0.85[ASN][1000 genomes]
rs149540	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149599	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152184	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152191	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152199	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs152202	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs152203	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs152209	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152215	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1562244	0.85[ASN][1000 genomes]
rs166005	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16890622	0.80[EUR][1000 genomes]
rs173523	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2034240	0.80[EUR][1000 genomes]
rs2289883	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247218	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247220	0.84[EUR][1000 genomes]
rs247221	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs247222	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247223	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247233	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247240	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247244	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247248	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247249	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247255	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs247265	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247267	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247268	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs247269	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247270	0.82[EUR][1000 genomes]
rs247273	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247275	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247494	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs264519	0.80[EUR][1000 genomes]
rs264520	0.80[EUR][1000 genomes]
rs264521	0.80[EUR][1000 genomes]
rs26631	0.88[ASN][1000 genomes]
rs26632	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26637	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26641	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26644	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27693	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28539215	0.86[ASN][1000 genomes]
rs28581963	0.86[ASN][1000 genomes]
rs28615140	0.82[ASN][1000 genomes]
rs34562047	0.85[ASN][1000 genomes]
rs3776615	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3776638	0.88[ASN][1000 genomes]
rs40110	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs438143	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6881888	0.88[ASN][1000 genomes]
rs7702634	0.81[EUR][1000 genomes]
rs7722692	0.87[ASN][1000 genomes]
rs7737525	0.87[ASN][1000 genomes]
rs784921	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs959899	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61709200-61770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:61709400-61727400	Weak transcription	Placenta	Placenta
3	chr5:61709400-61727400	Weak transcription	Pancreas	Pancrea
4	chr5:61709400-61763400	Weak transcription	Aorta	Aorta
5	chr5:61709600-61719400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:61709600-61723000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:61709600-61724600	Weak transcription	Fetal Stomach	stomach
8	chr5:61709600-61726400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr5:61709600-61728000	Weak transcription	Gastric	stomach
10	chr5:61709600-61738800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:61709600-61738800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:61709600-61739800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:61709600-61744000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr5:61709800-61727400	Weak transcription	HSMM	muscle
15	chr5:61709800-61728000	Weak transcription	Fetal Lung	lung
16	chr5:61709800-61728000	Weak transcription	Right Ventricle	heart
17	chr5:61709800-61728000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:61709800-61728200	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:61709800-61738800	Weak transcription	Fetal Kidney	kidney
20	chr5:61709800-61743800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:61709800-61746000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:61709800-61746600	Weak transcription	Fetal Thymus	thymus
23	chr5:61709800-61769000	Weak transcription	NH-A	brain
24	chr5:61709800-61809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:61710000-61715800	Weak transcription	HUVEC	blood vessel
26	chr5:61710000-61716200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:61710000-61717200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:61710000-61718400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:61710000-61721200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:61710000-61721400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:61710000-61727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:61710000-61727200	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:61710000-61727600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:61710000-61729000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:61710000-61734200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:61710000-61734200	Weak transcription	Fetal Intestine Small	intestine
37	chr5:61710000-61737400	Weak transcription	Fetal Intestine Large	intestine
38	chr5:61710000-61739000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:61710000-61746000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:61710200-61720400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:61710200-61728000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:61710200-61733400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:61710200-61738800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:61710200-61746000	Weak transcription	Primary B cells from cord blood	blood
45	chr5:61710400-61718400	Weak transcription	NHDF-Ad	bronchial
46	chr5:61710400-61733600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:61710400-61739000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:61710400-61746000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:61710600-61716000	Weak transcription	Brain Angular Gyrus	brain
50	chr5:61710600-61738800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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