Variant report

Variant	rs2241874
Chromosome Location	chr2:234247627-234247628
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	BCL3	chr2:234247534-234247800	GM12878	blood:	n/a	n/a
2	BCL3	chr2:234247428-234247832	GM12878	blood:	n/a	chr2:234247800-234247809
3	PBX3	chr2:234247543-234247751	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234159356..234161467-chr2:234246206..234249085,2	MCF-7	breast:
2	chr2:234242293..234245038-chr2:234245423..234247780,3	MCF-7	breast:

Variant related genes	Relation type
SAG	TF binding region
ENSG00000130561	Chromatin interaction
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1000141	0.86[CHB][hapmap]
rs10168355	0.82[ASN][1000 genomes]
rs1046974	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs13028996	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241873	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2304777	0.85[TSI][hapmap]
rs3792093	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs3792096	0.85[TSI][hapmap]
rs3792097	0.85[TSI][hapmap]
rs3792098	0.82[ASN][1000 genomes]
rs6431310	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6710735	0.85[TSI][hapmap]
rs6725503	0.88[ASN][1000 genomes]
rs6726046	0.81[YRI][hapmap]
rs6734243	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742218	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6756706	0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs745498	0.85[TSI][hapmap]
rs7608122	0.85[TSI][hapmap]
rs894100	0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2241874	SCARNA5	cis	parietal	SCAN
rs2241874	ATG16L1	cis	cerebellum	SCAN
rs2241874	FBXO36	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234237400-234249800	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:234241000-234249600	Enhancers	Primary B cells from cord blood	blood
3	chr2:234243000-234247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:234244600-234257800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:234246600-234249400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:234247000-234248200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:234247000-234248400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:234247000-234249200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:234247000-234249400	Enhancers	Hela-S3	cervix
10	chr2:234247200-234247800	Enhancers	Fetal Intestine Small	intestine
11	chr2:234247200-234248400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr2:234247200-234249400	Enhancers	HepG2	liver
13	chr2:234247400-234247800	Enhancers	Gastric	stomach
14	chr2:234247400-234247800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:234247400-234249200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:234247400-234249200	Enhancers	Stomach Mucosa	stomach
17	chr2:234247400-234251400	Weak transcription	K562	blood
18	chr2:234247600-234247800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:234247600-234247800	Enhancers	Small Intestine	intestine
20	chr2:234247600-234248200	Enhancers	Duodenum Mucosa	Duodenum
21	chr2:234247600-234248200	Enhancers	Fetal Intestine Large	intestine
22	chr2:234247600-234248200	Enhancers	GM12878-XiMat	blood
23	chr2:234247600-234257400	Weak transcription	Spleen	Spleen

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