Variant report

Variant	rs3950558
Chromosome Location	chr4:48020932-48020933
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48019190..48021605-chr4:48023120..48025588,2	K562	blood:
2	chr4:48019513..48022096-chr4:48074921..48077158,2	MCF-7	breast:
3	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170448	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10002500	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs10015582	0.85[YRI][hapmap]
rs10049713	0.81[YRI][hapmap]
rs10517204	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805163	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10938520	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11733288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371732	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1396051	0.89[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507913	0.86[ASN][1000 genomes]
rs1507914	0.86[ASN][1000 genomes]
rs16860680	0.85[YRI][hapmap]
rs178650	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1837518	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1866688	0.91[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.85[YRI][hapmap]
rs188901	0.88[ASN][1000 genomes]
rs1899060	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs224800	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2581493	0.86[ASN][1000 genomes]
rs2661513	0.83[JPT][hapmap]
rs28578328	0.80[ASN][1000 genomes]
rs28642966	0.91[ASW][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap]
rs28699496	0.82[ASN][1000 genomes]
rs3113881	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113882	0.85[ASN][1000 genomes]
rs321621	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321633	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321642	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs321644	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs321646	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4694880	0.89[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695326	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447603	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs6850603	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685636	0.86[ASN][1000 genomes]
rs9998800	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3950558	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48022600	Weak transcription	Gastric	stomach
2	chr4:48019800-48022600	Weak transcription	Small Intestine	intestine
3	chr4:48019800-48024200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:48019800-48024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:48019800-48026000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48019800-48026600	Weak transcription	NH-A	brain
7	chr4:48019800-48027600	Weak transcription	Placenta	Placenta
8	chr4:48019800-48030200	Weak transcription	Psoas Muscle	Psoas
9	chr4:48019800-48033800	Weak transcription	Pancreas	Pancrea
10	chr4:48019800-48033800	Weak transcription	Hela-S3	cervix
11	chr4:48019800-48034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:48019800-48034200	Weak transcription	HepG2	liver
13	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
15	chr4:48020000-48026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:48020000-48029200	Weak transcription	GM12878-XiMat	blood
17	chr4:48020200-48021000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:48020400-48021000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr4:48020400-48027600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:48020600-48022000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:48020600-48022400	Weak transcription	Liver	Liver
22	chr4:48020600-48022800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr4:48020600-48023000	Enhancers	Duodenum Mucosa	Duodenum
24	chr4:48020600-48026200	Weak transcription	Fetal Heart	heart
25	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
26	chr4:48020800-48021000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr4:48020800-48021600	Enhancers	Stomach Mucosa	stomach
28	chr4:48020800-48022400	Weak transcription	NHEK	skin
29	chr4:48020800-48024200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:48020800-48025000	Enhancers	Fetal Intestine Small	intestine
31	chr4:48020800-48025400	Enhancers	Fetal Intestine Large	intestine
32	chr4:48020800-48026600	Weak transcription	HMEC	breast

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