Variant report

Variant	rs6941673
Chromosome Location	chr6:55916571-55916572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1022539	0.92[JPT][hapmap]
rs1033478	0.92[JPT][hapmap]
rs12199712	0.92[JPT][hapmap]
rs12199742	0.92[JPT][hapmap]
rs1319112	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs13193925	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs13209836	0.90[JPT][hapmap]
rs1480	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1555097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1925141	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs1925143	0.92[JPT][hapmap]
rs1925147	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs1925149	0.92[JPT][hapmap]
rs1925179	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1925181	0.91[JPT][hapmap]
rs1925185	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs1925189	0.92[JPT][hapmap]
rs1980487	0.92[JPT][hapmap]
rs2038149	0.92[JPT][hapmap]
rs2038173	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2206674	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2328677	0.96[CEU][hapmap];0.92[JPT][hapmap];0.94[TSI][hapmap]
rs2397201	0.98[ASN][1000 genomes]
rs2397204	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2397208	0.84[JPT][hapmap]
rs2745366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2764046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2764052	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2841000	0.83[CEU][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs2841006	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2841007	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3817983	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs3846918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3846920	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs3846921	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3846922	0.92[JPT][hapmap]
rs3846923	0.92[JPT][hapmap]
rs3846924	0.92[JPT][hapmap]
rs3857611	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs3857612	0.92[JPT][hapmap]
rs3996940	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs4119567	0.92[JPT][hapmap]
rs4126558	0.92[JPT][hapmap]
rs4379279	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs4495274	0.92[JPT][hapmap]
rs4573075	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4596475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4599643	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4712112	0.89[ASN][1000 genomes]
rs4712113	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs4715574	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715575	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715585	0.92[JPT][hapmap]
rs4715591	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs4715597	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs6459128	0.92[JPT][hapmap]
rs6459136	0.92[JPT][hapmap]
rs66585712	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66953461	0.82[EUR][1000 genomes]
rs6909268	0.90[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs6914495	0.92[JPT][hapmap]
rs6927919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6933151	0.92[JPT][hapmap]
rs6939465	0.92[JPT][hapmap]
rs7774374	0.87[CEU][hapmap];0.92[JPT][hapmap]
rs9296824	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296828	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs9296830	0.80[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9357886	0.83[EUR][1000 genomes]
rs9357891	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs9367673	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370485	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs9370486	0.92[JPT][hapmap]
rs9382583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9382595	0.92[JPT][hapmap]
rs9396176	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs9475593	0.92[JPT][hapmap]
rs9475621	0.92[JPT][hapmap]
rs994667	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv830665	chr6:55755560-55920219	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1023687	chr6:55868611-55940255	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1020208	chr6:55870429-55932120	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv538227	chr6:55870429-55932120	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	esv3474014	chr6:55907505-55918211	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3474013	chr6:55907507-55918172	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3486610	chr6:55907534-55918254	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3474015	chr6:55907553-55918186	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3474016	chr6:55907647-55918110	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3486611	chr6:55907647-55918110	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1029182	chr6:55910866-55991956	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
15	esv3432353	chr6:55912873-55918277	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6941673	C6orf142	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55899200-55920400	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:55911800-55940800	Weak transcription	Left Ventricle	heart
3	chr6:55915200-55917000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:55915400-55916800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr6:55916000-55919000	Weak transcription	Osteobl	bone
6	chr6:55916000-55920200	Weak transcription	Fetal Lung	lung
7	chr6:55916000-55927000	Weak transcription	Fetal Stomach	stomach
8	chr6:55916200-55922200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:55916200-55923400	Weak transcription	Fetal Heart	heart

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