Variant report

Variant	rs17002829
Chromosome Location	chr4:78763139-78763140
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	chr4:78758087..78761671-chr4:78762539..78765213,4	K562	blood:
2	chr4:78762303..78763958-chr4:78782788..78784420,2	K562	blood:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 160 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs10005741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10007837	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1010728	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs10222901	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1039403	1.00[CHB][hapmap]
rs1039467	0.87[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs10428319	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs10856982	0.86[ASN][1000 genomes]
rs11097935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097965	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11097980	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs1156059	0.86[ASN][1000 genomes]
rs11721383	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11723029	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11723221	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11727993	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11729703	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11730329	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730403	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11732039	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs11733759	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734428	0.85[AMR][1000 genomes]
rs11737353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11737861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11939576	1.00[ASN][1000 genomes]
rs12108312	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs12510593	1.00[CHB][hapmap]
rs13111592	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13118459	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13131896	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137909	0.86[ASN][1000 genomes]
rs13138341	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13144225	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13144226	0.86[ASN][1000 genomes]
rs1402626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1521419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553386	0.87[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs1554457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002823	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002824	1.00[ASN][1000 genomes]
rs17002825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002828	1.00[ASN][1000 genomes]
rs17002831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813725	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1814033	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1847216	0.87[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs1980266	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030463	0.84[ASN][1000 genomes]
rs2102116	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2134048	0.92[CHB][hapmap]
rs2134459	0.85[AMR][1000 genomes]
rs2173869	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2174080	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2866444	0.80[AMR][1000 genomes]
rs2866688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2866689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2866690	1.00[CHB][hapmap]
rs28796999	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28891692	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3205281	0.92[CHB][hapmap]
rs3849580	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4078523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4304001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4331798	0.91[AMR][1000 genomes]
rs4365752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4410552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4417999	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4473672	0.91[AMR][1000 genomes]
rs4541532	0.86[ASN][1000 genomes]
rs4561950	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs4607246	0.92[ASN][1000 genomes]
rs4859506	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4859871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4859876	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4859878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859901	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs55673370	0.90[ASN][1000 genomes]
rs55694923	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55886549	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57221952	0.85[AMR][1000 genomes]
rs57246363	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57501818	0.88[ASN][1000 genomes]
rs57868780	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58054752	0.85[AMR][1000 genomes]
rs58218398	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58358199	0.93[ASN][1000 genomes]
rs60135456	0.98[ASN][1000 genomes]
rs6533239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6533269	0.86[ASN][1000 genomes]
rs6533270	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533271	0.86[ASN][1000 genomes]
rs6533272	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533274	0.87[ASN][1000 genomes]
rs6533290	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533358	0.81[AMR][1000 genomes]
rs6533359	0.85[AMR][1000 genomes]
rs6533374	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs6533376	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs6533382	0.81[JPT][hapmap]
rs6817305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6817823	0.86[ASN][1000 genomes]
rs6821826	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs6822317	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823465	0.81[ASN][1000 genomes]
rs6827822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6828302	0.86[ASN][1000 genomes]
rs6830993	0.91[AMR][1000 genomes]
rs6836627	0.88[ASN][1000 genomes]
rs6838630	0.88[ASN][1000 genomes]
rs6839504	1.00[CHB][hapmap]
rs6849922	0.87[ASN][1000 genomes]
rs6850049	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6850111	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6850590	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs6851286	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs6855336	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6857067	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6857479	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs72868269	1.00[ASN][1000 genomes]
rs72869573	0.80[ASN][1000 genomes]
rs73827437	0.99[ASN][1000 genomes]
rs73827443	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73827451	0.92[ASN][1000 genomes]
rs73827456	0.91[AMR][1000 genomes]
rs73827459	0.85[AMR][1000 genomes]
rs73827460	0.85[AMR][1000 genomes]
rs7439347	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7655949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7657658	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659122	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7661064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7663359	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7669988	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7671941	0.92[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7674744	1.00[CHB][hapmap]
rs7675586	0.85[ASN][1000 genomes]
rs7687170	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7687812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7689226	0.91[ASN][1000 genomes]
rs7692075	0.87[ASN][1000 genomes]
rs7693256	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7698246	0.82[JPT][hapmap]
rs885376	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9991424	0.85[AMR][1000 genomes]
rs9993942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9996218	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17002829	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78762800-78763200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:78763000-78764600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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