Variant report

Variant	rs6546323
Chromosome Location	chr2:67854444-67854445
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	chr2:67624303..67625839-chr2:67853938..67856689,2	MCF-7	breast:
2	chr2:67852630..67855318-chr2:67906179..67908434,2	K562	blood:

Variant related genes	Relation type
ENSG00000143971	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10490719	0.83[ASN][1000 genomes]
rs10490720	0.83[ASN][1000 genomes]
rs10490721	0.89[ASN][1000 genomes]
rs1107595	0.88[ASN][1000 genomes]
rs11126137	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11126139	0.86[ASN][1000 genomes]
rs11126140	0.88[ASN][1000 genomes]
rs11679082	0.90[ASN][1000 genomes]
rs11680000	0.89[ASN][1000 genomes]
rs11680926	0.91[ASN][1000 genomes]
rs11686555	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11693956	0.90[ASN][1000 genomes]
rs12328339	0.82[ASN][1000 genomes]
rs12616261	0.88[ASN][1000 genomes]
rs12619942	0.86[ASN][1000 genomes]
rs12621286	0.83[ASN][1000 genomes]
rs12624204	0.88[ASN][1000 genomes]
rs17033787	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17033788	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2270342	0.87[ASN][1000 genomes]
rs2270343	0.87[ASN][1000 genomes]
rs2270344	0.87[ASN][1000 genomes]
rs2270346	0.87[ASN][1000 genomes]
rs2270348	0.88[ASN][1000 genomes]
rs2861641	0.84[ASN][1000 genomes]
rs2861643	0.86[ASN][1000 genomes]
rs2861650	0.88[ASN][1000 genomes]
rs2861651	0.90[ASN][1000 genomes]
rs2861679	0.92[ASN][1000 genomes]
rs2861688	0.94[ASN][1000 genomes]
rs2861692	0.93[ASN][1000 genomes]
rs2861693	0.92[ASN][1000 genomes]
rs2861696	0.92[ASN][1000 genomes]
rs2861697	0.99[ASN][1000 genomes]
rs2861699	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2902020	0.88[ASN][1000 genomes]
rs3885079	0.84[ASN][1000 genomes]
rs4233940	0.84[ASN][1000 genomes]
rs4368311	0.88[ASN][1000 genomes]
rs4444509	0.90[ASN][1000 genomes]
rs4591326	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs4671185	0.84[ASN][1000 genomes]
rs4671186	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4671187	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4671188	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4671189	0.90[ASN][1000 genomes]
rs4671193	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671808	0.90[ASN][1000 genomes]
rs60735969	0.85[ASN][1000 genomes]
rs61004148	0.90[ASN][1000 genomes]
rs6721459	0.94[AFR][1000 genomes]
rs723712	0.90[ASN][1000 genomes]
rs72621572	0.88[ASN][1000 genomes]
rs72621573	0.91[ASN][1000 genomes]
rs72621574	0.92[ASN][1000 genomes]
rs7579880	0.82[AFR][1000 genomes]
rs7598674	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7598832	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9309400	0.93[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	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6546323	C2orf42	cis	cerebellum	SCAN
rs6546323	GMCL1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67852400-67854600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:67852400-67854600	Enhancers	NHDF-Ad	bronchial
3	chr2:67852400-67855000	Enhancers	HSMM	muscle
4	chr2:67853000-67854600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:67853200-67854600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:67853400-67854600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:67853400-67855000	Weak transcription	Fetal Stomach	stomach
8	chr2:67853400-67855000	Enhancers	HSMMtube	muscle
9	chr2:67853800-67855000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:67853800-67855200	Weak transcription	Fetal Muscle Leg	muscle

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