Variant report

Variant	rs27089
Chromosome Location	chr5:61697859-61697860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:61697820-61700282	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:61697842-61700273	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:61695775..61698135-chr5:61722484..61724142,2	K562	blood:
2	chr5:61685307..61687523-chr5:61697635..61699406,2	K562	blood:
3	chr5:61696503..61703698-chr5:61706632..61711868,15	MCF-7	breast:
4	chr5:61696900..61702493-chr5:61705289..61710261,23	K562	blood:
5	chr5:61679991..61682016-chr5:61697548..61699312,2	MCF-7	breast:
6	chr5:61697532..61701694-chr5:61703408..61710603,12	MCF-7	breast:
7	chr5:61571856..61574619-chr5:61696505..61699367,2	K562	blood:

No data

Variant related genes	Relation type
IPO11	TF binding region
ENSG00000086200	Chromatin interaction
ENSG00000086189	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10058598	0.80[ASN][1000 genomes]
rs10069988	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs101091	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1301064	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1301065	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13361219	0.82[ASN][1000 genomes]
rs152186	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152204	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152205	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152210	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247225	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247227	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247231	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247232	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247237	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247241	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247242	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247243	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247250	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247251	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247254	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247259	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247262	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247264	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247266	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247479	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26635	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs26639	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26642	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs27448	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27449	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs27931	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35119	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35348760	0.82[ASN][1000 genomes]
rs4145851	0.81[ASN][1000 genomes]
rs767159	0.82[ASN][1000 genomes]
rs784916	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs784918	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61642600-61699200	Weak transcription	Gastric	stomach
2	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:61661800-61698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
6	chr5:61666800-61698000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:61667600-61698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:61668000-61698000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:61672000-61698600	Weak transcription	Stomach Mucosa	stomach
10	chr5:61676800-61699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:61682200-61699000	Weak transcription	Colonic Mucosa	Colon
12	chr5:61684200-61698400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr5:61686800-61698200	Weak transcription	Fetal Brain Male	brain
14	chr5:61688200-61698000	Strong transcription	Fetal Muscle Leg	muscle
15	chr5:61690200-61698000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:61690400-61698000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:61690400-61698800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr5:61690400-61699000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:61690400-61699000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:61690600-61698000	Weak transcription	HepG2	liver
21	chr5:61690600-61698800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:61691400-61698000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:61691800-61698200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:61692400-61698400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:61693000-61698200	Strong transcription	Ovary	ovary
26	chr5:61693200-61698200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:61694200-61698000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:61694600-61698000	Weak transcription	Brain Anterior Caudate	brain
29	chr5:61694600-61698200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:61694600-61698200	Weak transcription	Brain Angular Gyrus	brain
31	chr5:61694600-61698200	Weak transcription	Psoas Muscle	Psoas
32	chr5:61694600-61698400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:61694800-61698000	Weak transcription	Fetal Kidney	kidney
34	chr5:61694800-61698000	Weak transcription	Osteobl	bone
35	chr5:61694800-61698200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:61694800-61698200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:61695800-61698200	Strong transcription	Primary B cells from cord blood	blood
38	chr5:61696000-61698200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:61696400-61698000	Weak transcription	Fetal Lung	lung
40	chr5:61696400-61698400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:61696600-61698400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:61696800-61698000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:61696800-61699000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:61697000-61698000	Weak transcription	Brain Hippocampus Middle	brain
45	chr5:61697000-61698000	Weak transcription	A549	lung
46	chr5:61697000-61698200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr5:61697000-61698200	Weak transcription	Fetal Brain Female	brain
48	chr5:61697000-61698200	Weak transcription	Fetal Intestine Large	intestine
49	chr5:61697000-61698200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:61697000-61698400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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