Variant report

Variant	rs1883139
Chromosome Location	chr1:174840900-174840901
allele	A/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	NFIC	chr1:174840669-174841458	GM12878	blood:	n/a	n/a
2	NFATC1	chr1:174840870-174841458	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:174840757-174841508	GM12878	blood:	n/a	n/a
4	SP1	chr1:174840893-174841500	H1-hESC	embryonic stem cell:	n/a	n/a
5	HDAC2	chr1:174840891-174841387	H1-hESC	embryonic stem cell:	n/a	chr1:174841289-174841303 chr1:174841285-174841299 chr1:174841288-174841302 chr1:174841287-174841301
6	CREB1	chr1:174840847-174841421	GM12878	blood:	n/a	n/a
7	FOXM1	chr1:174840834-174841404	GM12878	blood:	n/a	n/a
8	BCLAF1	chr1:174840820-174841313	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174793359..174795191-chr1:174840553..174843195,2	MCF-7	breast:
2	chr1:174835636..174838063-chr1:174838882..174841494,2	K562	blood:
3	chr1:174838028..174841189-chr1:174966759..174968847,3	K562	blood:
4	chr1:174838711..174843709-chr1:174844718..174847483,6	K562	blood:
5	chr1:174839381..174842561-chr1:174854989..174856827,3	K562	blood:
6	chr1:174838028..174843892-chr1:174965943..174969167,5	K562	blood:
7	chr1:174840446..174846237-chr1:174965266..174970099,5	MCF-7	breast:
8	chr1:174838711..174843357-chr1:174844135..174848349,5	K562	blood:

Variant related genes	Relation type
RABGAP1L	TF binding region
ENSG00000116161	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000252552	Chromatin interaction

Extended variants
information (count: 191 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:190)

rs_ID	r²[population]
rs1012182	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034462	0.81[ASN][1000 genomes]
rs10494492	0.85[EUR][1000 genomes]
rs1058741	0.81[ASN][1000 genomes]
rs10798324	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798327	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912828	0.81[EUR][1000 genomes]
rs10912829	0.81[EUR][1000 genomes]
rs10912843	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912853	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912855	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11800350	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806066	0.89[ASN][1000 genomes]
rs11806996	0.81[EUR][1000 genomes]
rs11809803	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810508	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063093	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065825	0.81[EUR][1000 genomes]
rs12078839	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094876	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1231826	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1231827	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1231829	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1329281	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149099	0.81[EUR][1000 genomes]
rs1540207	0.84[EUR][1000 genomes]
rs1613634	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618207	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618408	0.82[ASN][1000 genomes]
rs1622802	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162815	0.82[ASN][1000 genomes]
rs1653630	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1653634	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16847335	0.86[EUR][1000 genomes]
rs16847337	0.86[EUR][1000 genomes]
rs16847624	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17302033	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17302367	0.81[ASN][1000 genomes]
rs1754350	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1754352	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1754353	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1754354	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1754360	0.82[ASN][1000 genomes]
rs17842156	0.86[EUR][1000 genomes]
rs17842157	0.86[EUR][1000 genomes]
rs1793292	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793294	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793295	0.88[EUR][1000 genomes]
rs1793298	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793305	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793307	0.82[ASN][1000 genomes]
rs1793310	0.82[ASN][1000 genomes]
rs1793313	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1793316	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793318	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793320	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1813136	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1894198	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894199	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894201	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894680	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923818	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193082	0.86[EUR][1000 genomes]
rs2003378	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060158	0.84[EUR][1000 genomes]
rs2146564	0.86[EUR][1000 genomes]
rs2157567	0.81[ASN][1000 genomes]
rs2163628	0.90[EUR][1000 genomes]
rs2183202	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568096	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568098	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2760057	0.86[EUR][1000 genomes]
rs2760058	0.81[EUR][1000 genomes]
rs2771401	0.85[EUR][1000 genomes]
rs2860725	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2861005	0.86[EUR][1000 genomes]
rs2861006	0.86[EUR][1000 genomes]
rs2981892	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2981893	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2981896	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987872	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987873	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987875	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987876	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987880	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117838	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3117843	0.86[EUR][1000 genomes]
rs3118982	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118986	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118987	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3118990	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332767	0.87[EUR][1000 genomes]
rs332768	0.87[EUR][1000 genomes]
rs332779	0.88[EUR][1000 genomes]
rs332781	0.87[EUR][1000 genomes]
rs332782	0.87[EUR][1000 genomes]
rs332786	0.88[EUR][1000 genomes]
rs332793	0.85[EUR][1000 genomes]
rs332797	0.84[EUR][1000 genomes]
rs332800	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs332801	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs332802	0.80[EUR][1000 genomes]
rs332806	0.81[EUR][1000 genomes]
rs333422	0.87[EUR][1000 genomes]
rs333432	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs333436	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs333438	0.87[EUR][1000 genomes]
rs333452	0.83[EUR][1000 genomes]
rs333454	0.83[EUR][1000 genomes]
rs36127331	0.85[EUR][1000 genomes]
rs3766697	0.81[ASN][1000 genomes]
rs3862941	0.85[EUR][1000 genomes]
rs392307	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs395109	0.81[EUR][1000 genomes]
rs398350	0.88[EUR][1000 genomes]
rs399530	0.87[EUR][1000 genomes]
rs411665	0.84[EUR][1000 genomes]
rs4480415	0.82[EUR][1000 genomes]
rs458242	0.88[EUR][1000 genomes]
rs459078	0.82[ASN][1000 genomes]
rs460878	0.87[EUR][1000 genomes]
rs464540	0.86[EUR][1000 genomes]
rs464635	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4651114	0.81[EUR][1000 genomes]
rs4651205	0.97[ASN][1000 genomes]
rs4651231	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651235	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652797	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467437	0.88[EUR][1000 genomes]
rs55667039	0.85[EUR][1000 genomes]
rs55688014	0.86[EUR][1000 genomes]
rs55774740	0.81[ASN][1000 genomes]
rs55793234	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55844798	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57289077	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58030712	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60482554	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60811893	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425298	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425300	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425301	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425304	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6425306	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667107	0.81[EUR][1000 genomes]
rs6671196	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6671782	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66836419	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684229	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684515	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686872	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687616	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689153	0.81[EUR][1000 genomes]
rs6690754	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693979	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696465	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6700953	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67054007	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67133776	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67203477	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67903803	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72715273	0.81[EUR][1000 genomes]
rs72715281	0.86[EUR][1000 genomes]
rs72715292	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72715294	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72715300	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717608	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717616	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717617	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72717618	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717630	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717637	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72717649	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72717650	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717653	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72717661	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72717670	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74128535	0.81[ASN][1000 genomes]
rs7516353	0.81[EUR][1000 genomes]
rs7516410	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521109	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7531032	0.81[ASN][1000 genomes]
rs7543147	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554767	0.81[ASN][1000 genomes]
rs913686	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913687	0.82[ASN][1000 genomes]
rs913688	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989424	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1883139	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs1883139	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174819200-174843600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:174832000-174843000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:174833000-174841400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:174836800-174843600	Weak transcription	Left Ventricle	heart
5	chr1:174838600-174843400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:174838600-174847400	Weak transcription	Esophagus	oesophagus
7	chr1:174839000-174841000	Weak transcription	Primary B cells from cord blood	blood
8	chr1:174839000-174841000	Enhancers	GM12878-XiMat	blood
9	chr1:174839600-174843400	Weak transcription	Stomach Mucosa	stomach
10	chr1:174840000-174843600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:174840200-174842200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr1:174840200-174843000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:174840400-174841400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:174840400-174841800	Enhancers	NHEK	skin
15	chr1:174840400-174842200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:174840400-174842400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:174840600-174841000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:174840600-174841200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:174840600-174841200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:174840600-174841800	Enhancers	HMEC	breast
21	chr1:174840600-174842000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:174840600-174843000	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:174840600-174846200	Enhancers	K562	blood
24	chr1:174840600-174846400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:174840800-174841200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:174840800-174841200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:174840800-174841400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:174840800-174841800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:174840800-174841800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links