Variant report

Variant	rs6533374
Chromosome Location	chr4:78915841-78915842
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78909839..78911739-chr4:78914254..78917095,2	MCF-7	breast:
2	chr4:78915334..78916174-chr4:79437913..79438840,4	MCF-7	breast:
3	chr4:78915311..78916190-chr4:79437915..79438836,3	K562	blood:

Variant related genes	Relation type
ENSG00000248640	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1010728	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10222901	0.92[CHB][hapmap]
rs1039467	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10428319	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10856991	0.95[ASN][1000 genomes]
rs11097935	0.81[AMR][1000 genomes]
rs11097965	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs11097980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11721383	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs11723221	0.89[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs11727993	0.81[AMR][1000 genomes]
rs11729703	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11731374	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs11732039	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11733759	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs11734428	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11737353	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs11737861	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs11937191	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12108312	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12507708	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12650649	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13131896	0.81[AMR][1000 genomes]
rs13144225	0.81[AMR][1000 genomes]
rs1501373	0.81[AMR][1000 genomes]
rs1502879	1.00[ASN][1000 genomes]
rs1502880	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521419	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs1553386	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1554457	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs17002823	0.81[AMR][1000 genomes]
rs17002825	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs17002829	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs1814033	0.81[AMR][1000 genomes]
rs1847215	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847216	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1910304	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1980266	0.81[AMR][1000 genomes]
rs2036458	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2088993	1.00[CEU][hapmap]
rs2102190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2134459	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2174078	0.86[ASN][1000 genomes]
rs2174079	0.98[ASN][1000 genomes]
rs2174080	0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2866688	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2903291	0.81[AMR][1000 genomes]
rs35896758	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4304001	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4331798	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4365752	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs4388114	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4410552	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4417999	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4473672	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4546268	0.80[ASN][1000 genomes]
rs4561950	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4859515	0.96[ASN][1000 genomes]
rs4859876	0.81[AMR][1000 genomes]
rs4859878	0.81[AMR][1000 genomes]
rs4859894	0.96[ASN][1000 genomes]
rs4859896	0.96[ASN][1000 genomes]
rs4859897	0.96[ASN][1000 genomes]
rs4859898	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859899	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859900	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859901	0.85[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55886549	0.81[AMR][1000 genomes]
rs56138517	0.80[ASN][1000 genomes]
rs57221952	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57246363	0.81[AMR][1000 genomes]
rs57896992	0.80[ASN][1000 genomes]
rs58054752	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6533270	0.81[AMR][1000 genomes]
rs6533272	0.81[AMR][1000 genomes]
rs6533358	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533359	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533382	0.84[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6817305	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs6821826	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6822317	0.91[CHB][hapmap];0.81[AMR][1000 genomes]
rs6827822	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs6830993	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6832015	0.80[ASN][1000 genomes]
rs6835181	0.85[CEU][hapmap]
rs6850049	0.81[AMR][1000 genomes]
rs6850590	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6851286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854989	0.80[ASN][1000 genomes]
rs6857067	0.81[AMR][1000 genomes]
rs6857479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73827456	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73827459	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73827460	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7439347	0.92[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs7655949	0.81[AMR][1000 genomes]
rs7656319	0.82[ASN][1000 genomes]
rs7657658	0.85[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs7659122	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7661064	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs7663359	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7669988	0.81[AMR][1000 genomes]
rs7671432	0.96[ASN][1000 genomes]
rs7671941	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7673642	0.82[ASN][1000 genomes]
rs7687170	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7687812	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs7698246	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs7699987	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs950263	0.96[ASN][1000 genomes]
rs950264	0.96[ASN][1000 genomes]
rs9991424	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	nsv1004772	chr4:78906866-78976561	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6533374	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78915000-78916000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:78915000-78916000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:78915000-78916000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr4:78915200-78916000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:78915200-78916000	Enhancers	Fetal Kidney	kidney
6	chr4:78915200-78916000	Enhancers	Fetal Lung	lung
7	chr4:78915200-78916200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr4:78915200-78916200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:78915200-78916200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr4:78915200-78916200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:78915200-78916200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:78915200-78916200	Enhancers	HSMMtube	muscle
13	chr4:78915200-78917000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:78915400-78916000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:78915400-78916400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:78915400-78916400	Flanking Active TSS	HepG2	liver
17	chr4:78915400-78917200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr4:78915600-78916000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:78915600-78916000	Enhancers	Left Ventricle	heart
20	chr4:78915800-78916000	Enhancers	Lung	lung
21	chr4:78915800-78916200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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