Variant report

Variant	rs247225
Chromosome Location	chr5:61662555-61662556
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	chr5:61662283..61664182-chr5:61672693..61674594,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10051719	0.82[AFR][1000 genomes]
rs10062387	0.84[AFR][1000 genomes]
rs10067200	0.83[AFR][1000 genomes]
rs10069988	0.82[ASN][1000 genomes]
rs10075026	0.83[AFR][1000 genomes]
rs101091	0.82[ASN][1000 genomes]
rs10461472	0.81[ASN][1000 genomes]
rs10471546	0.81[ASN][1000 genomes]
rs10939937	0.82[ASN][1000 genomes]
rs12515967	0.81[ASN][1000 genomes]
rs12655269	0.81[AFR][1000 genomes]
rs12659793	0.84[AFR][1000 genomes]
rs12659814	0.84[AFR][1000 genomes]
rs12696990	0.81[ASN][1000 genomes]
rs1301064	0.84[ASN][1000 genomes]
rs1301065	0.84[ASN][1000 genomes]
rs1309156	0.84[ASN][1000 genomes]
rs13361219	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs152186	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs152204	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs152205	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs152210	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs174647	0.81[ASN][1000 genomes]
rs1862527	0.84[AFR][1000 genomes]
rs1995782	0.82[AFR][1000 genomes]
rs2289883	0.84[ASN][1000 genomes]
rs247218	0.84[ASN][1000 genomes]
rs247220	0.82[ASN][1000 genomes]
rs247221	0.83[ASN][1000 genomes]
rs247222	0.84[ASN][1000 genomes]
rs247223	0.83[ASN][1000 genomes]
rs247227	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247231	0.87[ASN][1000 genomes]
rs247232	0.87[ASN][1000 genomes]
rs247237	0.87[ASN][1000 genomes]
rs247241	0.91[ASN][1000 genomes]
rs247242	0.94[ASN][1000 genomes]
rs247243	0.94[ASN][1000 genomes]
rs247250	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs247251	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247254	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247255	0.81[ASN][1000 genomes]
rs247259	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs247262	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs247264	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247265	0.84[ASN][1000 genomes]
rs247266	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247267	0.84[ASN][1000 genomes]
rs247268	0.82[ASN][1000 genomes]
rs247269	0.84[ASN][1000 genomes]
rs247273	0.84[ASN][1000 genomes]
rs247275	0.84[ASN][1000 genomes]
rs247479	0.87[ASN][1000 genomes]
rs264519	0.81[ASN][1000 genomes]
rs264521	0.81[ASN][1000 genomes]
rs264523	0.81[ASN][1000 genomes]
rs264528	0.81[ASN][1000 genomes]
rs264531	0.81[ASN][1000 genomes]
rs26635	0.84[ASN][1000 genomes]
rs26639	0.82[ASN][1000 genomes]
rs26642	0.82[ASN][1000 genomes]
rs27089	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs27448	0.86[ASN][1000 genomes]
rs27449	0.82[ASN][1000 genomes]
rs27931	0.83[ASN][1000 genomes]
rs28589513	0.82[AFR][1000 genomes]
rs35119	0.86[ASN][1000 genomes]
rs35348760	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776615	0.81[ASN][1000 genomes]
rs3846467	0.83[AFR][1000 genomes]
rs4145851	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs438143	0.82[ASN][1000 genomes]
rs4700009	0.81[ASN][1000 genomes]
rs56049450	0.81[EUR][1000 genomes]
rs56317447	0.82[AFR][1000 genomes]
rs767159	0.81[ASN][1000 genomes]
rs7700569	0.81[ASN][1000 genomes]
rs7702634	0.81[ASN][1000 genomes]
rs784916	0.87[ASN][1000 genomes]
rs784918	0.87[ASN][1000 genomes]
rs9291758	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61607800-61669400	Weak transcription	NHLF	lung
2	chr5:61622400-61676000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:61624000-61669600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:61629200-61676400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:61629600-61665000	Weak transcription	Esophagus	oesophagus
6	chr5:61631200-61669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:61631200-61669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:61631200-61676000	Weak transcription	Lung	lung
9	chr5:61638600-61671200	Weak transcription	Small Intestine	intestine
10	chr5:61639800-61684200	Weak transcription	Psoas Muscle	Psoas
11	chr5:61641400-61682400	Weak transcription	Fetal Heart	heart
12	chr5:61642400-61665400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:61642600-61688400	Weak transcription	Right Ventricle	heart
15	chr5:61642600-61696000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:61642600-61699200	Weak transcription	Gastric	stomach
17	chr5:61643000-61697000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:61643800-61663200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:61643800-61666000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:61643800-61680600	Strong transcription	Placenta	Placenta
21	chr5:61644000-61671600	Weak transcription	Stomach Mucosa	stomach
22	chr5:61644000-61689000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:61645400-61689200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:61646800-61673800	Weak transcription	Fetal Brain Male	brain
25	chr5:61647000-61690000	Weak transcription	Spleen	Spleen
26	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr5:61650000-61667800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr5:61651000-61666000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:61651200-61665400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:61653600-61665200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:61653600-61666000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:61656000-61665400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:61656200-61663200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:61656200-61665200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:61656800-61664200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr5:61656800-61687800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:61657000-61662600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:61657000-61663200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:61657000-61663400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:61657000-61663400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:61657000-61664200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:61657000-61664400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr5:61657000-61665800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:61657200-61663000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:61657200-61663800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:61657600-61662600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr5:61657600-61663000	Strong transcription	Brain Germinal Matrix	brain
49	chr5:61657800-61663600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr5:61658400-61664200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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