Variant report

Variant	rs2397201
Chromosome Location	chr6:55918736-55918737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:55886603..55887384-chr6:55918244..55919071,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1022539	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1033478	0.92[JPT][hapmap]
rs12199712	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs12199742	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs1319111	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs1319112	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13193925	0.96[CEU][hapmap];0.92[JPT][hapmap]
rs13209836	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs1480	0.84[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap]
rs1555097	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1925141	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1925143	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs1925147	1.00[JPT][hapmap]
rs1925149	0.92[JPT][hapmap]
rs1925179	0.92[JPT][hapmap];0.91[MEX][hapmap]
rs1925181	0.91[JPT][hapmap]
rs1925185	0.96[CEU][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs1925189	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs1980487	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2038149	0.92[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs2038150	0.92[CEU][hapmap]
rs2038173	0.83[ASN][1000 genomes]
rs2206674	0.80[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap]
rs2328677	0.92[JPT][hapmap]
rs2397204	0.92[JPT][hapmap]
rs2397208	0.87[CEU][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2745366	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2764046	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2764052	0.80[CEU][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap]
rs2841000	0.92[JPT][hapmap]
rs2841006	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs2841007	0.80[CEU][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap]
rs3817983	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs3846918	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3846920	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs3846921	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3846922	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs3846923	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs3846924	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs3857611	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3857612	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs3996940	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4119567	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs4126558	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs4379279	0.92[JPT][hapmap]
rs4495274	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs4573075	0.80[CEU][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap]
rs4596475	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4599643	0.85[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap]
rs4712112	0.87[ASN][1000 genomes]
rs4712113	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4715574	0.96[ASN][1000 genomes]
rs4715575	0.96[ASN][1000 genomes]
rs4715585	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs4715591	0.86[JPT][hapmap]
rs4715597	1.00[JPT][hapmap]
rs6459128	0.87[CEU][hapmap];0.92[JPT][hapmap]
rs6459133	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs6459136	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs66585712	0.84[ASN][1000 genomes]
rs6909268	0.90[JPT][hapmap]
rs6914495	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs6927919	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6933151	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs6939465	0.92[JPT][hapmap]
rs6941673	0.98[ASN][1000 genomes]
rs761105	0.81[CEU][hapmap]
rs7774374	0.92[JPT][hapmap]
rs9296824	0.96[ASN][1000 genomes]
rs9296828	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs9296830	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs9357891	0.92[JPT][hapmap]
rs9367673	0.96[ASN][1000 genomes]
rs9370485	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs9370486	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs9382583	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9382595	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs9396176	0.86[JPT][hapmap]
rs9475593	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs9475621	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs994667	0.80[CEU][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2397201	GCLC	cis	parietal	SCAN

Chromatin state (count:7 , 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	chr6:55916000-55919000	Weak transcription	Osteobl	bone
4	chr6:55916000-55920200	Weak transcription	Fetal Lung	lung
5	chr6:55916000-55927000	Weak transcription	Fetal Stomach	stomach
6	chr6:55916200-55922200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:55916200-55923400	Weak transcription	Fetal Heart	heart

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