Variant report

Variant	rs4140572
Chromosome Location	chr22:32809162-32809163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs11089557	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11089560	0.82[EUR][1000 genomes]
rs11089564	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11635	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11912349	0.90[ASN][1000 genomes]
rs12160141	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12160986	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12628702	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs136471	0.94[AMR][1000 genomes]
rs1543320	0.81[CHB][hapmap]
rs16987625	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990258	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990262	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990269	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16990428	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16990430	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1810450	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2014356	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049946	0.84[CHB][hapmap]
rs2072815	0.87[CHB][hapmap]
rs2072816	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2076041	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076045	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281034	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2281035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281036	0.87[CHB][hapmap]
rs2294311	0.98[ASN][1000 genomes]
rs2294312	0.83[ASN][1000 genomes]
rs2294313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2294314	0.98[ASN][1000 genomes]
rs2413110	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2413111	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2413113	0.86[CHB][hapmap]
rs28404482	0.88[AMR][1000 genomes]
rs2899184	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2899185	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]
rs35207231	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs45593940	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4577392	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749408	0.84[EUR][1000 genomes]
rs5749409	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749410	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749411	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749412	0.81[JPT][hapmap]
rs5749413	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5749414	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749416	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs5749421	0.80[ASN][1000 genomes]
rs5749426	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs5749427	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749428	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5749429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749433	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749436	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs5753988	0.91[AMR][1000 genomes]
rs5754000	0.97[AMR][1000 genomes]
rs5754001	0.94[AMR][1000 genomes]
rs5754003	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes]
rs5754005	0.94[AMR][1000 genomes]
rs5754006	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754007	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754008	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754009	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes]
rs5754010	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754011	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754012	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754017	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754018	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754019	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754021	0.91[AMR][1000 genomes]
rs5754023	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754025	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754027	0.81[JPT][hapmap]
rs5754029	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754030	0.82[JPT][hapmap]
rs5754032	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754033	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5754035	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754036	0.81[JPT][hapmap]
rs5754037	0.81[JPT][hapmap]
rs5754039	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754040	0.82[JPT][hapmap]
rs5754042	0.80[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754044	0.82[JPT][hapmap]
rs5754045	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754046	0.82[EUR][1000 genomes]
rs5754047	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754048	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754050	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5754063	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs5754065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754066	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs58028985	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58500302	0.91[AMR][1000 genomes]
rs59895149	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5994562	0.84[CHB][hapmap]
rs5998434	0.89[AMR][1000 genomes]
rs5998451	0.81[JPT][hapmap]
rs5998453	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5998457	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5998459	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5998463	0.82[JPT][hapmap]
rs5998471	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs5998475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5998478	0.83[CHB][hapmap]
rs713790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72137940	0.83[ASN][1000 genomes]
rs72617300	0.86[AMR][1000 genomes]
rs72617301	0.89[AMR][1000 genomes]
rs72617302	0.94[AMR][1000 genomes]
rs72620403	0.89[AMR][1000 genomes]
rs72620404	0.94[AMR][1000 genomes]
rs72620405	0.94[AMR][1000 genomes]
rs72620406	0.94[AMR][1000 genomes]
rs72620407	0.94[AMR][1000 genomes]
rs72620408	0.94[AMR][1000 genomes]
rs7287452	0.82[CHB][hapmap]
rs7292163	0.82[EUR][1000 genomes]
rs737779	0.96[CHB][hapmap];0.84[ASN][1000 genomes]
rs738267	0.81[JPT][hapmap]
rs742096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1055701	chr22:32806595-32845403	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4140572	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32807400-32809200	Active TSS	Stomach Smooth Muscle	stomach
2	chr22:32807600-32809200	Active TSS	Brain Substantia Nigra	brain
3	chr22:32807600-32809200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr22:32808200-32818000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr22:32808400-32818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr22:32808600-32809200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
7	chr22:32808600-32810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr22:32808800-32809200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr22:32808800-32809200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr22:32808800-32809200	Enhancers	Liver	Liver
11	chr22:32808800-32809200	Enhancers	Rectal Smooth Muscle	rectum
12	chr22:32808800-32809200	Enhancers	K562	blood
13	chr22:32808800-32809400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr22:32808800-32809400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr22:32808800-32810000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr22:32808800-32810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr22:32808800-32810000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr22:32808800-32810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:32808800-32810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr22:32808800-32810200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr22:32808800-32810600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:32809000-32809200	Enhancers	HepG2	liver
23	chr22:32809000-32810000	Weak transcription	HMEC	breast
24	chr22:32809000-32810000	Weak transcription	NHEK	skin
25	chr22:32809000-32814000	Weak transcription	GM12878-XiMat	blood
26	chr22:32809000-32817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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