Variant report

Variant	rs6700953
Chromosome Location	chr1:174843057-174843058
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	BATF	chr1:174842987-174843210	GM12878	blood:	n/a	chr1:174843129-174843140
2	RUNX3	chr1:174842909-174843248	GM12878	blood:	n/a	n/a
3	NFIC	chr1:174842929-174844751	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	chr1:174838711..174843709-chr1:174844718..174847483,6	K562	blood:
3	chr1:174838028..174843892-chr1:174965943..174969167,5	K562	blood:
4	chr1:174840446..174846237-chr1:174965266..174970099,5	MCF-7	breast:
5	chr1:174838711..174843357-chr1:174844135..174848349,5	K562	blood:

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

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1012182	0.97[ASN][1000 genomes]
rs10798324	0.82[ASN][1000 genomes]
rs10798327	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912823	0.82[EUR][1000 genomes]
rs10912843	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912853	0.92[ASN][1000 genomes]
rs10912854	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10912855	0.92[ASN][1000 genomes]
rs11800350	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11806066	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11809803	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810508	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063093	0.97[ASN][1000 genomes]
rs12067463	0.82[EUR][1000 genomes]
rs12078839	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12094876	0.92[ASN][1000 genomes]
rs1231826	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1231827	0.93[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];0.99[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	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1622802	0.82[ASN][1000 genomes]
rs162815	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1653630	0.82[ASN][1000 genomes]
rs1653634	0.82[ASN][1000 genomes]
rs1653636	0.85[EUR][1000 genomes]
rs16847624	0.87[ASN][1000 genomes]
rs17302033	0.92[ASN][1000 genomes]
rs1754350	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1754352	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1754353	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1754354	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1754360	0.87[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	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1793307	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793310	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1793313	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793315	0.84[EUR][1000 genomes]
rs1793316	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1793318	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1813136	0.82[ASN][1000 genomes]
rs1883139	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894198	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894199	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894201	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[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	0.82[EUR][1000 genomes]
rs2156854	0.83[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2981893	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2981896	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987872	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987873	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987875	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987876	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987880	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3117838	0.82[ASN][1000 genomes]
rs3118982	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3118986	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3118987	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3118990	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs332763	0.88[EUR][1000 genomes]
rs332764	0.88[EUR][1000 genomes]
rs332772	0.88[EUR][1000 genomes]
rs332784	0.87[EUR][1000 genomes]
rs332798	0.86[EUR][1000 genomes]
rs332800	0.82[ASN][1000 genomes]
rs332801	0.82[ASN][1000 genomes]
rs333423	0.86[EUR][1000 genomes]
rs333432	0.82[ASN][1000 genomes]
rs333436	0.82[ASN][1000 genomes]
rs333437	0.86[EUR][1000 genomes]
rs333453	0.82[EUR][1000 genomes]
rs333471	0.88[EUR][1000 genomes]
rs392307	0.82[ASN][1000 genomes]
rs459078	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs464635	0.84[ASN][1000 genomes]
rs4651205	0.88[AMR][1000 genomes];0.94[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]
rs57289077	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58030712	0.92[ASN][1000 genomes]
rs60482554	0.92[ASN][1000 genomes]
rs60811893	0.82[ASN][1000 genomes]
rs6425298	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425300	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425301	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425303	0.87[AMR][1000 genomes];0.92[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	0.88[AMR][1000 genomes];0.93[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	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6687616	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6690754	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693979	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696465	0.82[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	0.97[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	0.88[AMR][1000 genomes];0.93[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	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913686	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913687	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs913688	0.82[ASN][1000 genomes]
rs9425787	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989424	0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6700953	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:32 , 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	chr1:174836800-174843600	Weak transcription	Left Ventricle	heart
3	chr1:174838600-174843400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:174838600-174847400	Weak transcription	Esophagus	oesophagus
5	chr1:174839600-174843400	Weak transcription	Stomach Mucosa	stomach
6	chr1:174840000-174843600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:174840600-174846200	Enhancers	K562	blood
8	chr1:174840600-174846400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:174841200-174843400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:174841400-174843400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:174841400-174846400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:174842000-174846600	Weak transcription	HSMMtube	muscle
13	chr1:174842200-174843400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:174842200-174843400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:174842200-174843600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:174842200-174844200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:174842200-174844400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:174842600-174843400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:174842800-174843200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:174842800-174843400	Enhancers	Primary B cells from cord blood	blood
21	chr1:174843000-174843200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr1:174843000-174843200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:174843000-174843200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr1:174843000-174843400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:174843000-174843400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:174843000-174843400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:174843000-174843400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:174843000-174843400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:174843000-174843400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:174843000-174843400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:174843000-174843600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:174843000-174843600	Flanking Active TSS	GM12878-XiMat	blood

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