Variant report

Variant	rs1894198
Chromosome Location	chr1:174804531-174804532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174803637..174805618-chr1:174962090..174964287,2	K562	blood:
2	chr1:174804519..174806652-chr1:174968482..174970506,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 164 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1012182	0.97[ASN][1000 genomes]
rs10798324	0.82[ASN][1000 genomes]
rs10798327	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912823	0.82[EUR][1000 genomes]
rs10912843	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912853	0.92[ASN][1000 genomes]
rs10912854	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10912855	0.92[ASN][1000 genomes]
rs11800350	0.97[ASN][1000 genomes]
rs11806066	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11809803	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810508	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063093	0.97[ASN][1000 genomes]
rs12067463	0.82[EUR][1000 genomes]
rs12078839	0.97[ASN][1000 genomes]
rs12094876	0.92[ASN][1000 genomes]
rs1231826	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1231827	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1231829	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329281	0.82[ASN][1000 genomes]
rs1613634	0.82[ASN][1000 genomes]
rs1618207	0.82[ASN][1000 genomes]
rs1618408	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1622802	0.82[ASN][1000 genomes]
rs162815	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1653630	0.82[ASN][1000 genomes]
rs1653634	0.82[ASN][1000 genomes]
rs1653636	0.83[EUR][1000 genomes]
rs16847624	0.87[ASN][1000 genomes]
rs17302033	0.92[ASN][1000 genomes]
rs1754350	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1754352	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1754353	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1754354	0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1754360	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793292	0.82[ASN][1000 genomes]
rs1793294	0.82[ASN][1000 genomes]
rs1793298	0.82[ASN][1000 genomes]
rs1793305	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1793307	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793310	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793313	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793315	0.83[EUR][1000 genomes]
rs1793316	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1793318	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1813136	0.82[ASN][1000 genomes]
rs1883139	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894201	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894680	0.92[ASN][1000 genomes]
rs1923818	0.82[ASN][1000 genomes]
rs2003378	0.97[ASN][1000 genomes]
rs2156853	0.81[EUR][1000 genomes]
rs2156854	0.82[EUR][1000 genomes]
rs2183202	0.92[ASN][1000 genomes]
rs2568096	0.82[ASN][1000 genomes]
rs2568098	0.82[ASN][1000 genomes]
rs2860725	0.82[ASN][1000 genomes]
rs2981892	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2981893	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2981896	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987872	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987873	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987875	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987876	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2987880	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3117838	0.82[ASN][1000 genomes]
rs3118982	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3118986	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3118987	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3118990	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs332763	0.86[EUR][1000 genomes]
rs332764	0.86[EUR][1000 genomes]
rs332772	0.86[EUR][1000 genomes]
rs332784	0.85[EUR][1000 genomes]
rs332798	0.84[EUR][1000 genomes]
rs332800	0.82[ASN][1000 genomes]
rs332801	0.82[ASN][1000 genomes]
rs333423	0.85[EUR][1000 genomes]
rs333432	0.82[ASN][1000 genomes]
rs333436	0.82[ASN][1000 genomes]
rs333437	0.85[EUR][1000 genomes]
rs333453	0.82[EUR][1000 genomes]
rs333471	0.86[EUR][1000 genomes]
rs392307	0.82[ASN][1000 genomes]
rs459078	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs464635	0.84[ASN][1000 genomes]
rs4651205	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651231	0.92[ASN][1000 genomes]
rs4651235	0.97[ASN][1000 genomes]
rs4652797	0.82[ASN][1000 genomes]
rs55793234	0.92[ASN][1000 genomes]
rs55844798	0.82[ASN][1000 genomes]
rs56292878	0.81[EUR][1000 genomes]
rs57289077	0.92[ASN][1000 genomes]
rs58030712	0.92[ASN][1000 genomes]
rs60482554	0.92[ASN][1000 genomes]
rs60811893	0.82[ASN][1000 genomes]
rs6425298	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425300	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425301	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425303	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6425306	0.92[ASN][1000 genomes]
rs6671196	0.92[ASN][1000 genomes]
rs6671272	0.85[ASN][1000 genomes]
rs6671782	0.92[ASN][1000 genomes]
rs6675528	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6677874	0.82[EUR][1000 genomes]
rs66836419	0.92[ASN][1000 genomes]
rs6684229	0.92[ASN][1000 genomes]
rs6684515	0.92[ASN][1000 genomes]
rs6686872	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6687616	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6690754	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693979	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696465	0.82[ASN][1000 genomes]
rs6700953	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67054007	0.87[ASN][1000 genomes]
rs67133776	0.88[ASN][1000 genomes]
rs67203477	0.92[ASN][1000 genomes]
rs67903803	0.88[ASN][1000 genomes]
rs72715292	0.82[ASN][1000 genomes]
rs72715294	0.82[ASN][1000 genomes]
rs72715300	0.82[ASN][1000 genomes]
rs72717608	0.82[ASN][1000 genomes]
rs72717616	0.82[ASN][1000 genomes]
rs72717617	0.87[ASN][1000 genomes]
rs72717618	0.82[ASN][1000 genomes]
rs72717630	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72717637	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717649	0.95[ASN][1000 genomes]
rs72717650	0.97[ASN][1000 genomes]
rs72717653	0.92[ASN][1000 genomes]
rs72717661	0.92[ASN][1000 genomes]
rs72717670	0.87[ASN][1000 genomes]
rs7514183	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7516410	0.92[ASN][1000 genomes]
rs7521109	0.82[ASN][1000 genomes]
rs7543147	0.97[ASN][1000 genomes]
rs7547658	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913686	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913687	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs913688	0.82[ASN][1000 genomes]
rs9425787	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989424	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	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
4	esv1844208	chr1:174764839-174818547	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1847553	chr1:174764839-174818547	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv437280	chr1:174794144-174805122	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv437291	chr1:174794144-174805122	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv437302	chr1:174794144-174805122	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1815488	chr1:174794144-174818547	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv1821003	chr1:174794144-174818547	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1844568	chr1:174794144-174818547	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv872556	chr1:174794420-174819336	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv2764238	chr1:174794978-174808605	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1844237	chr1:174796670-174818547	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv548217	chr1:174797867-174812326	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv872557	chr1:174800121-174819336	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv872558	chr1:174802731-174818547	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv274970	chr1:174803606-174804967	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv872559	chr1:174803606-174819336	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1894198	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174782200-174813000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:174784800-174806600	Weak transcription	HSMMtube	muscle
3	chr1:174796600-174833400	Weak transcription	Primary B cells from cord blood	blood
4	chr1:174798400-174810800	Weak transcription	GM12878-XiMat	blood
5	chr1:174801800-174808400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:174802000-174804800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:174802200-174806800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:174803800-174804600	Weak transcription	Brain Anterior Caudate	brain

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