Variant report

Variant	rs59684347
Chromosome Location	chr2:209117297-209117298
allele	C/T
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	chr2:209116778-209117373	HepG2	liver:	n/a	n/a
2	EBF1	chr2:209117077-209117716	GM12878	blood:	n/a	chr2:209117225-209117236 chr2:209117225-209117235
3	CCNT2	chr2:209116932-209117300	K562	blood:	n/a	n/a
4	POLR2A	chr2:209099467-209120161	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:209115314..209118296-chr2:209118564..209121392,2	MCF-7	breast:
2	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:
3	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
4	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:

Variant related genes	Relation type
IDH1-AS1	TF binding region
ENSG00000138413	Chromatin interaction
ENSG00000115020	Chromatin interaction
ENSG00000231908	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10174541	1.00[ASN][1000 genomes]
rs10186350	1.00[ASN][1000 genomes]
rs10194539	1.00[ASN][1000 genomes]
rs10198535	1.00[ASN][1000 genomes]
rs10202116	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497897	1.00[ASN][1000 genomes]
rs10497898	1.00[ASN][1000 genomes]
rs11554137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685614	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895188	1.00[ASN][1000 genomes]
rs11898653	1.00[ASN][1000 genomes]
rs11901959	1.00[ASN][1000 genomes]
rs13412043	1.00[ASN][1000 genomes]
rs34218846	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928183	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59522113	1.00[ASN][1000 genomes]
rs6435435	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66887797	1.00[ASN][1000 genomes]
rs67171462	1.00[ASN][1000 genomes]
rs67202912	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67581965	1.00[ASN][1000 genomes]
rs67669827	1.00[ASN][1000 genomes]
rs72976889	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72989243	1.00[ASN][1000 genomes]
rs73056463	1.00[ASN][1000 genomes]
rs73070950	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070958	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070962	1.00[ASN][1000 genomes]
rs7557303	1.00[ASN][1000 genomes]
rs7565247	0.94[EUR][1000 genomes]
rs7609093	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9646838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209093000-209118400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:209099800-209118000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:209100200-209118000	Strong transcription	Fetal Thymus	thymus
4	chr2:209100600-209117800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:209100800-209117800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:209100800-209117800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr2:209101000-209118000	Strong transcription	Placenta	Placenta
8	chr2:209101200-209118000	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr2:209101200-209118400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:209101400-209117600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr2:209101400-209117800	Strong transcription	Primary T cells from cord blood	blood
12	chr2:209102000-209117800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:209103200-209118200	Strong transcription	NH-A	brain
14	chr2:209103400-209118200	Strong transcription	NHDF-Ad	bronchial
15	chr2:209104200-209118000	Weak transcription	Right Ventricle	heart
16	chr2:209104800-209118400	Weak transcription	Aorta	Aorta
17	chr2:209105000-209118800	Weak transcription	Gastric	stomach
18	chr2:209106800-209118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:209106800-209118400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:209106800-209118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:209108000-209117600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:209108800-209118400	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr2:209112200-209117600	Strong transcription	NHLF	lung
24	chr2:209112800-209118800	Weak transcription	Lung	lung
25	chr2:209113400-209118000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:209113400-209118000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:209113400-209118000	Weak transcription	Pancreas	Pancrea
28	chr2:209113600-209118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:209113800-209118600	Weak transcription	Colonic Mucosa	Colon
30	chr2:209114000-209117400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:209114000-209118400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:209114200-209118200	Strong transcription	HSMM	muscle
33	chr2:209114200-209118400	Weak transcription	Fetal Stomach	stomach
34	chr2:209114200-209118400	Weak transcription	Small Intestine	intestine
35	chr2:209114200-209118400	Weak transcription	Thymus	Thymus
36	chr2:209114200-209118800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:209114200-209118800	Weak transcription	Esophagus	oesophagus
38	chr2:209114200-209118800	Weak transcription	Spleen	Spleen
39	chr2:209114400-209118400	Weak transcription	Psoas Muscle	Psoas
40	chr2:209114600-209117400	Genic enhancers	HUVEC	blood vessel
41	chr2:209114600-209118400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:209114800-209118400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:209115000-209117600	Genic enhancers	A549	lung
44	chr2:209115000-209117800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr2:209115000-209118000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr2:209115000-209118000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:209115200-209118400	Enhancers	Primary B cells from cord blood	blood
48	chr2:209115200-209118400	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr2:209115400-209117600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:209115400-209117600	Genic enhancers	Dnd41	blood

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