Variant report

Variant	rs62166129
Chromosome Location	chr2:78644002-78644003
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	FOXA2	chr2:78643529-78644646	HepG2	liver:	n/a	chr2:78643949-78643961
2	FOXA1	chr2:78643648-78644425	HepG2	liver:	n/a	chr2:78643949-78643961
3	FOXA2	chr2:78643783-78644256	HepG2	liver:	n/a	chr2:78643949-78643961
4	FOXA1	chr2:78643718-78644455	HepG2	liver:	n/a	chr2:78643949-78643961
5	FOSL2	chr2:78643805-78644293	HepG2	liver:	n/a	chr2:78643925-78643932 chr2:78644193-78644203 chr2:78644190-78644198 chr2:78643924-78643932 chr2:78644193-78644203 chr2:78644190-78644198 chr2:78644190-78644197
6	MXI1	chr2:78643589-78644126	HepG2	liver:	n/a	n/a
7	EP300	chr2:78643480-78645885	SK-N-SH	brain:	n/a	chr2:78643948-78643958 chr2:78644190-78644199 chr2:78643549-78643563
8	JUND	chr2:78643746-78644729	HepG2	liver:	n/a	chr2:78643925-78643932 chr2:78644193-78644203 chr2:78644190-78644198 chr2:78643924-78643932 chr2:78644193-78644203 chr2:78644190-78644198 chr2:78644190-78644197
9	EP300	chr2:78643729-78644062	HepG2	liver:	n/a	chr2:78643948-78643958
10	EP300	chr2:78643901-78644101	HepG2	liver:	n/a	chr2:78643948-78643958
11	MAFK	chr2:78643366-78644150	HepG2	liver:	n/a	chr2:78643373-78643388 chr2:78643561-78643572
12	STAT3	chr2:78643794-78644051	Hela-S3	cervix:	n/a	n/a
13	MAFF	chr2:78643418-78644056	HepG2	liver:	n/a	chr2:78643558-78643576
14	FOXA1	chr2:78643775-78644062	HepG2	liver:	n/a	chr2:78643949-78643961
15	STAT3	chr2:78643832-78644032	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr2:78643721-78644215	HepG2	liver:	n/a	chr2:78643948-78643958 chr2:78644190-78644199
17	TCF7L2	chr2:78643646-78644140	Hela-S3	cervix:	n/a	chr2:78643957-78643971
18	JUN	chr2:78643821-78644072	HepG2	liver:	n/a	chr2:78643925-78643932 chr2:78643924-78643932
19	TCF7L2	chr2:78643834-78644169	PANC-1	pancreas:	n/a	chr2:78643957-78643971
20	ARID3A	chr2:78643666-78644757	HepG2	liver:	n/a	n/a
21	RXRA	chr2:78643804-78644097	HepG2	liver:	n/a	chr2:78643924-78643933
22	TCF7L2	chr2:78643767-78644149	MCF-7	breast:	n/a	chr2:78643957-78643971
23	RCOR1	chr2:78643827-78644027	HepG2	liver:	n/a	n/a
24	CEBPB	chr2:78643741-78644061	HepG2	liver:	n/a	n/a
25	FOXA1	chr2:78643610-78644216	HepG2	liver:	n/a	chr2:78643949-78643961
26	TCF7L2	chr2:78643772-78644121	Hela-S3	cervix:	n/a	chr2:78643957-78643971
27	TCF7L2	chr2:78643751-78644151	HepG2	liver:	n/a	chr2:78643957-78643971

Variant related genes	Relation type
CYCSP6	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10166453	0.88[EUR][1000 genomes]
rs10200062	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203802	0.97[EUR][1000 genomes]
rs10451628	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425208	0.88[EUR][1000 genomes]
rs13425834	0.88[EUR][1000 genomes]
rs13426270	0.88[EUR][1000 genomes]
rs1516259	0.97[EUR][1000 genomes]
rs55884007	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56044358	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56114016	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56268498	0.81[EUR][1000 genomes]
rs62164669	0.85[EUR][1000 genomes]
rs62164671	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62164672	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62164673	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62164674	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62164675	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62164676	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62164693	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62164697	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62166119	0.97[EUR][1000 genomes]
rs62166128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62166131	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62166136	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62166137	0.88[EUR][1000 genomes]
rs62166138	0.81[EUR][1000 genomes]
rs62166139	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62166142	0.88[EUR][1000 genomes]
rs62166143	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62166144	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62166581	0.89[ASN][1000 genomes]
rs6721735	0.85[EUR][1000 genomes]
rs72808856	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808867	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72808897	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72810614	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72810616	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72810617	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72810620	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72820954	0.89[AFR][1000 genomes]
rs9309533	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001461	chr2:78091352-78673948	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2757811	chr2:78126389-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2759068	chr2:78126389-78711032	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1005115	chr2:78307330-78673948	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1002464	chr2:78308336-78658280	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv535787	chr2:78308336-78658280	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1010116	chr2:78399683-78660165	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv998161	chr2:78404349-78660165	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1000078	chr2:78410008-78660165	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1014232	chr2:78413760-79034119	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv535788	chr2:78413760-79034119	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv916498	chr2:78429997-79340383	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv582273	chr2:78432494-78978011	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1014484	chr2:78504497-78972453	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1002114	chr2:78511306-78743191	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv535789	chr2:78511306-78743191	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv834271	chr2:78519702-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv3584761	chr2:78545020-79430628	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv874359	chr2:78546919-78680056	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv874360	chr2:78546919-78691068	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv998961	chr2:78574081-79150087	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv1002687	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv535790	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv874361	chr2:78582650-78691068	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv874362	chr2:78582650-78805852	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv874363	chr2:78608101-78702648	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv428052	chr2:78615333-79075603	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv874364	chr2:78640246-78857870	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78643600-78644600	Enhancers	Brain Hippocampus Middle	brain
2	chr2:78643600-78645400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:78643600-78645400	Enhancers	HepG2	liver
4	chr2:78643800-78644600	Enhancers	Brain Substantia Nigra	brain
5	chr2:78643800-78645400	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links