Variant report

Variant	rs246198
Chromosome Location	chr5:61697202-61697203
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	chr5:61697048-61697216	K562	blood:	n/a	n/a
2	POLR2A	chr5:61697121-61697213	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:61695775..61698135-chr5:61722484..61724142,2	K562	blood:
2	chr5:61696503..61703698-chr5:61706632..61711868,15	MCF-7	breast:
3	chr5:61696900..61702493-chr5:61705289..61710261,23	K562	blood:
4	chr5:61571856..61574619-chr5:61696505..61699367,2	K562	blood:

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

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11740652	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11747516	0.82[ASN][1000 genomes]
rs12655562	0.82[ASN][1000 genomes]
rs13155253	0.82[ASN][1000 genomes]
rs13156073	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13156695	0.82[ASN][1000 genomes]
rs13174779	0.82[ASN][1000 genomes]
rs13190153	0.83[ASN][1000 genomes]
rs153859	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153860	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153864	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153866	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153869	0.82[ASN][1000 genomes]
rs153873	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16875037	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16890618	0.82[ASN][1000 genomes]
rs16890628	0.82[ASN][1000 genomes]
rs16890634	0.82[ASN][1000 genomes]
rs16890651	0.82[ASN][1000 genomes]
rs173530	0.82[ASN][1000 genomes]
rs17382217	0.96[EUR][1000 genomes]
rs181784	0.85[ASN][1000 genomes]
rs2272291	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2441115	0.85[ASN][1000 genomes]
rs246200	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2463079	0.82[ASN][1000 genomes]
rs247477	0.85[ASN][1000 genomes]
rs247480	0.82[ASN][1000 genomes]
rs247481	0.85[ASN][1000 genomes]
rs247484	0.82[ASN][1000 genomes]
rs26619	0.85[ASN][1000 genomes]
rs26620	0.82[ASN][1000 genomes]
rs27090	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs32047	0.82[ASN][1000 genomes]
rs34220654	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34596001	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35011	0.85[ASN][1000 genomes]
rs35012	0.85[ASN][1000 genomes]
rs35054	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35055	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35058	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35238667	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35572300	0.82[ASN][1000 genomes]
rs35699711	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3776612	0.82[ASN][1000 genomes]
rs3776614	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3822487	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40109	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs417822	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4289514	0.82[ASN][1000 genomes]
rs7446543	0.82[ASN][1000 genomes]
rs785665	0.82[ASN][1000 genomes]
rs785666	0.82[ASN][1000 genomes]
rs785667	0.82[ASN][1000 genomes]
rs814169	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	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:61661800-61698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
9	chr5:61666800-61698000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:61667600-61697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:61667600-61698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:61668000-61698000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:61672000-61698600	Weak transcription	Stomach Mucosa	stomach
14	chr5:61675000-61697800	Weak transcription	Small Intestine	intestine
15	chr5:61676800-61697800	Weak transcription	Right Atrium	heart
16	chr5:61676800-61699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:61679600-61697600	Strong transcription	Liver	Liver
18	chr5:61682200-61699000	Weak transcription	Colonic Mucosa	Colon
19	chr5:61682800-61697800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:61683400-61697800	Weak transcription	Fetal Heart	heart
21	chr5:61684200-61698400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr5:61686800-61698200	Weak transcription	Fetal Brain Male	brain
23	chr5:61687600-61697800	Weak transcription	Brain Substantia Nigra	brain
24	chr5:61688200-61698000	Strong transcription	Fetal Muscle Leg	muscle
25	chr5:61689600-61697800	Strong transcription	Fetal Stomach	stomach
26	chr5:61689800-61697800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:61689800-61697800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:61690200-61698000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:61690400-61697800	Weak transcription	NHLF	lung
30	chr5:61690400-61698000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:61690400-61698800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr5:61690400-61699000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:61690400-61699000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:61690600-61698000	Weak transcription	HepG2	liver
35	chr5:61690600-61698800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:61691000-61697800	Weak transcription	HMEC	breast
37	chr5:61691400-61698000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:61691600-61697800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:61691800-61697800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:61691800-61698200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:61692400-61697400	Strong transcription	K562	blood
42	chr5:61692400-61697800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:61692400-61697800	Weak transcription	Aorta	Aorta
44	chr5:61692400-61698400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:61693000-61697400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:61693000-61698200	Strong transcription	Ovary	ovary
47	chr5:61693200-61698200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:61693800-61697800	Strong transcription	NHEK	skin
49	chr5:61694200-61698000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:61694600-61697800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links