Variant report

Variant	rs4144738
Chromosome Location	chr8:130760850-130760851
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	chr8:130760414..130761002-chr8:130838183..130839066,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10092783	0.89[ASW][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes]
rs10104593	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10110525	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1074286	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10808583	0.83[ASN][1000 genomes]
rs10956490	0.82[ASN][1000 genomes]
rs11984666	0.86[ASN][1000 genomes]
rs12678545	0.83[AMR][1000 genomes]
rs16904150	0.88[LWK][hapmap]
rs2062078	1.00[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs3886937	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3886938	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs4130415	0.84[ASN][1000 genomes]
rs4144736	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];0.97[ASN][1000 genomes]
rs4144737	0.88[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236747	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4285452	0.88[GIH][hapmap]
rs4335095	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4345520	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4425724	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4518624	0.89[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4527833	0.84[TSI][hapmap]
rs4571702	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4733557	0.80[AMR][1000 genomes]
rs4733724	0.83[ASN][1000 genomes]
rs4733725	0.84[ASN][1000 genomes]
rs4733726	0.86[ASN][1000 genomes]
rs4733727	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4733728	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4733729	1.00[ASW][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs4733732	1.00[CHB][hapmap]
rs4733734	0.91[AMR][1000 genomes]
rs5006712	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60228607	0.86[ASN][1000 genomes]
rs6470763	0.83[ASN][1000 genomes]
rs6470764	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs6470765	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6651255	0.84[ASN][1000 genomes]
rs6985118	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6986256	0.85[ASN][1000 genomes]
rs7004355	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7341636	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7388479	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7814941	0.83[ASN][1000 genomes]
rs7815955	0.83[ASN][1000 genomes]
rs7816131	0.83[ASN][1000 genomes]
rs7816342	0.84[ASN][1000 genomes]
rs7816625	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7822056	0.92[AMR][1000 genomes]
rs7826493	0.87[ASN][1000 genomes]
rs7828785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7841981	0.86[ASN][1000 genomes]
rs7846627	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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	nsv428524	chr8:130731660-130894467	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4144738	GSDMC	cis	Muscle Skeletal	GTEx
rs4144738	GSDMC	cis	Esophagus Mucosa	GTEx
rs4144738	MLZE	cis	uninvolved skin	skin_eQTL
rs4144738	MLZE	cis	normal skin	skin_eQTL
rs4144738	MLZE	cis	lesional skin	skin_eQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:130754600-130766000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr8:130755600-130764000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:130758200-130765400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:130758400-130763800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:130759200-130765800	Strong transcription	NHEK	skin
6	chr8:130759400-130761600	Weak transcription	Spleen	Spleen
7	chr8:130759800-130765800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:130760200-130765800	Strong transcription	Esophagus	oesophagus

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