Variant report

Variant	rs6688713
Chromosome Location	chr1:215253603-215253604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:215252610-215253603	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:215252626-215253667	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:215163670..215166597-chr1:215252249..215254651,2	MCF-7	breast:

Variant related genes	Relation type
KCNK2	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10127521	0.91[AMR][1000 genomes]
rs10127656	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10746454	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes]
rs10746455	0.95[CEU][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes]
rs10779639	0.85[CHB][hapmap]
rs10779640	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10779642	0.95[CEU][hapmap];0.91[AMR][1000 genomes]
rs10779643	0.95[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes]
rs10779644	0.84[CHB][hapmap]
rs10779645	0.83[CHB][hapmap]
rs10779647	0.85[CHB][hapmap]
rs10779649	0.95[CEU][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs10779651	0.86[MEX][hapmap];0.83[YRI][hapmap]
rs10864150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864152	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10864154	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11120495	0.95[CEU][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes]
rs11120497	0.89[AMR][1000 genomes]
rs11120499	0.85[CHB][hapmap]
rs11120500	0.91[AMR][1000 genomes]
rs11120508	0.85[CHB][hapmap]
rs11120511	0.84[CHB][hapmap]
rs11120513	0.85[CHB][hapmap]
rs1112101	0.95[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs12031308	0.89[CHB][hapmap]
rs12039875	0.85[CHB][hapmap]
rs12120091	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs12121761	0.85[CHB][hapmap]
rs12135076	0.95[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes]
rs12141874	0.95[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs12143339	0.85[CHB][hapmap]
rs12410041	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs12567520	0.80[CEU][hapmap]
rs12742137	0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1339405	0.85[CHB][hapmap]
rs1339406	0.84[CHB][hapmap]
rs1361340	0.82[MKK][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes]
rs1416647	0.95[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs1578137	0.84[AMR][1000 genomes]
rs2363552	0.86[YRI][hapmap]
rs2363554	0.83[CHB][hapmap]
rs2363556	0.95[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs2363557	0.95[CEU][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes]
rs2363558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363560	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2363564	0.85[CHB][hapmap]
rs2363565	0.85[CHB][hapmap]
rs2363566	0.95[CEU][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs2363567	0.95[CEU][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs2885812	0.88[CHB][hapmap]
rs2885813	0.91[AMR][1000 genomes]
rs2885815	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4262516	0.81[AMR][1000 genomes]
rs4269745	0.91[AMR][1000 genomes]
rs4271184	0.90[CHB][hapmap]
rs4300189	0.95[CEU][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes]
rs4303048	0.95[CEU][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes]
rs4375232	0.90[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs4411107	0.85[CHB][hapmap]
rs4497183	0.84[CHB][hapmap]
rs4509553	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs4531266	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4548407	0.83[AMR][1000 genomes]
rs4556330	0.90[CHB][hapmap]
rs4571941	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4607848	0.93[AMR][1000 genomes]
rs4634877	0.90[CHB][hapmap]
rs4655277	0.82[YRI][hapmap]
rs4655278	0.87[AMR][1000 genomes]
rs4655391	0.85[CHB][hapmap]
rs4655392	0.85[CHB][hapmap]
rs4655393	0.90[CEU][hapmap]
rs4655395	0.90[CEU][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes]
rs61818297	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61818299	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6657313	0.95[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs6662353	0.95[CEU][hapmap];0.95[MEX][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes]
rs6666828	0.85[CHB][hapmap]
rs6667764	0.85[CHB][hapmap]
rs6672978	0.84[CHB][hapmap]
rs6673739	0.81[CEU][hapmap]
rs6675926	0.95[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes]
rs6678758	0.90[AMR][1000 genomes]
rs6684084	0.82[YRI][hapmap]
rs6695967	0.93[CEU][hapmap];0.91[AMR][1000 genomes]
rs6696333	0.95[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes]
rs6699161	0.80[CHB][hapmap]
rs7410928	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7417100	0.85[CHB][hapmap]
rs7513709	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7516689	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535436	0.86[YRI][hapmap]
rs7540029	0.86[AMR][1000 genomes]
rs7541543	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7547655	0.91[ASW][hapmap];0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7549136	0.85[CHB][hapmap]
rs7551415	0.85[AMR][1000 genomes]
rs7551562	0.86[YRI][hapmap]
rs7555013	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555727	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9793690	0.83[AMR][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	esv2754411	chr1:215235605-215281605	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6688713	SYT14	cis	parietal	SCAN
rs6688713	FDX1	trans	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215252600-215254200	Enhancers	NHDF-Ad	bronchial
2	chr1:215253400-215254400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:215253400-215255000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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