Variant report

Variant	rs1998700
Chromosome Location	chr6:56032664-56032665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1011277	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1016719	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs1022539	0.93[LWK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs11970688	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193925	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs13209836	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs1320996	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1474698	0.88[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925139	0.81[AFR][1000 genomes]
rs1925145	0.85[CEU][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1925148	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1925152	0.88[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs1925153	0.88[YRI][hapmap]
rs1925165	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs1925166	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925170	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1925174	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925175	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925185	0.95[LWK][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs1980487	0.93[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs1998699	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038149	0.93[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs2038150	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs2076473	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2223598	0.85[CEU][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap]
rs2235735	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2397203	0.96[CEU][hapmap]
rs3823468	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs3846919	0.92[CEU][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs3846922	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs3846924	0.81[YRI][hapmap]
rs3846926	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3899394	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4119567	0.93[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs4126558	0.81[YRI][hapmap]
rs4140573	0.83[AFR][1000 genomes]
rs4140574	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4140575	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4310058	0.84[CEU][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4374814	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4452633	0.84[EUR][1000 genomes]
rs4490668	0.83[AFR][1000 genomes]
rs4607420	0.89[AFR][1000 genomes]
rs4612164	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4712116	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4712120	0.88[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs4715577	0.92[CEU][hapmap]
rs4715580	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715583	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715584	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715589	0.83[AFR][1000 genomes]
rs4715590	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715594	0.85[CEU][hapmap]
rs4715596	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6459130	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6459134	0.84[AFR][1000 genomes]
rs6920461	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6922057	0.90[AFR][1000 genomes]
rs6926301	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6927562	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6936386	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs761104	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761105	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764517	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741903	0.85[CEU][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7776118	0.86[CEU][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs926534	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs926535	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296827	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9296831	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9296832	0.88[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296833	0.85[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9349804	0.88[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9357887	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9357892	0.89[AFR][1000 genomes]
rs9357893	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357897	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9367676	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9370479	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs9370482	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9382584	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382595	0.80[YRI][hapmap]
rs9396173	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9396175	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9396176	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs9396183	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9475556	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs9475558	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9475564	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9475565	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9475583	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475586	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475641	0.84[CEU][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1998700	GCM1	cis	cerebellum	SCAN
rs1998700	ICK	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55984000-56037000	Weak transcription	Fetal Kidney	kidney
2	chr6:56013000-56036400	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:56021600-56033200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:56021800-56033000	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:56021800-56033000	Weak transcription	Fetal Stomach	stomach
6	chr6:56021800-56035800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:56021800-56036800	Weak transcription	Placenta	Placenta
8	chr6:56021800-56053200	Weak transcription	Aorta	Aorta
9	chr6:56027400-56033200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:56028800-56035400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:56031200-56033400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:56031600-56033400	Weak transcription	NHEK	skin
13	chr6:56032000-56033400	Weak transcription	Osteobl	bone
14	chr6:56032000-56035000	Weak transcription	Fetal Lung	lung
15	chr6:56032400-56033400	Weak transcription	NHDF-Ad	bronchial

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