Variant report

Variant	rs247259
Chromosome Location	chr5:61696635-61696636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:61696250-61696882	K562	blood:	n/a	n/a
2	POLR2A	chr5:61696484-61696992	GM12892	blood:	n/a	n/a
3	POLR2A	chr5:61696577-61697199	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:61695775..61698135-chr5:61722484..61724142,2	K562	blood:
2	chr5:61694523..61696770-chr5:61697647..61700221,3	MCF-7	breast:
3	chr5:61696503..61703698-chr5:61706632..61711868,15	MCF-7	breast:
4	chr5:61571856..61574619-chr5:61696505..61699367,2	K562	blood:

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

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10058598	0.83[ASN][1000 genomes]
rs10069988	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs101091	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12517326	0.81[ASN][1000 genomes]
rs1301064	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1301065	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13361219	0.85[ASN][1000 genomes]
rs152186	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152204	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152205	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152210	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16890800	0.82[ASN][1000 genomes]
rs247225	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs247227	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs247231	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247232	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247237	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247241	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247242	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247243	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247250	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247251	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247254	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs247255	0.81[AMR][1000 genomes]
rs247262	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247264	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247266	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs247479	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs26635	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26639	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26642	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27089	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27448	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27449	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27931	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35119	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35348760	0.85[ASN][1000 genomes]
rs4145851	0.84[ASN][1000 genomes]
rs767159	0.85[ASN][1000 genomes]
rs784916	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs784918	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9632387	0.82[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	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:61642600-61699200	Weak transcription	Gastric	stomach
3	chr5:61643000-61697000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:61661800-61698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
10	chr5:61666800-61698000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:61667000-61697200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr5:61667400-61697200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:61667600-61697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:61667600-61698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:61668000-61698000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:61668600-61697000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:61670000-61697200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:61672000-61698600	Weak transcription	Stomach Mucosa	stomach
19	chr5:61675000-61697800	Weak transcription	Small Intestine	intestine
20	chr5:61676800-61697800	Weak transcription	Right Atrium	heart
21	chr5:61676800-61699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:61679600-61697000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:61679600-61697600	Strong transcription	Liver	Liver
24	chr5:61680000-61697200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:61680000-61697200	Strong transcription	Adipose Nuclei	Adipose
26	chr5:61680200-61697000	Strong transcription	Primary T cells from cord blood	blood
27	chr5:61680200-61697000	Strong transcription	Fetal Intestine Large	intestine
28	chr5:61680400-61697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:61682000-61697000	Strong transcription	Placenta	Placenta
30	chr5:61682200-61699000	Weak transcription	Colonic Mucosa	Colon
31	chr5:61682800-61697800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:61683400-61697800	Weak transcription	Fetal Heart	heart
33	chr5:61683800-61697200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:61684200-61698400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr5:61686200-61697000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:61686800-61698200	Weak transcription	Fetal Brain Male	brain
37	chr5:61687400-61697200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:61687600-61697800	Weak transcription	Brain Substantia Nigra	brain
39	chr5:61688200-61698000	Strong transcription	Fetal Muscle Leg	muscle
40	chr5:61689600-61697800	Strong transcription	Fetal Stomach	stomach
41	chr5:61689800-61697000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr5:61689800-61697800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:61689800-61697800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:61690200-61698000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:61690400-61697800	Weak transcription	NHLF	lung
46	chr5:61690400-61698000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr5:61690400-61698800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:61690400-61699000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:61690400-61699000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr5:61690600-61698000	Weak transcription	HepG2	liver

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