Variant report

Variant	rs1339219
Chromosome Location	chr1:217172392-217172393
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:217167662..217170376-chr1:217171384..217173746,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1025650	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1030853	0.87[ASN][1000 genomes]
rs10492954	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10492957	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10495038	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779288	0.86[YRI][hapmap]
rs10863285	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs10863286	0.82[ASW][hapmap];0.91[GIH][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs11117737	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11117738	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11117745	0.98[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11572472	0.82[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs12025193	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029369	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12040129	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043713	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12121739	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12758444	0.83[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339214	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1339215	0.93[ASN][1000 genomes]
rs1339216	0.93[ASN][1000 genomes]
rs1436885	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1436886	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1436887	0.87[ASN][1000 genomes]
rs1561189	0.88[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1561190	0.87[ASN][1000 genomes]
rs1816565	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1836964	0.91[ASN][1000 genomes]
rs1865920	0.87[ASN][1000 genomes]
rs1865921	0.87[ASN][1000 genomes]
rs2028097	0.91[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2118148	0.91[ASN][1000 genomes]
rs2118149	0.88[ASN][1000 genomes]
rs2118150	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2164612	0.89[ASN][1000 genomes]
rs2437880	0.87[ASN][1000 genomes]
rs2576207	0.93[ASN][1000 genomes]
rs2576210	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2576211	0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2576212	0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2576214	0.87[ASN][1000 genomes]
rs2576216	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2576217	0.87[ASN][1000 genomes]
rs2576218	0.87[ASN][1000 genomes]
rs2576219	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2576220	0.88[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2576221	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2576222	0.88[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2576223	0.87[ASN][1000 genomes]
rs2576224	0.87[ASN][1000 genomes]
rs2576225	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2789554	0.91[ASN][1000 genomes]
rs2789561	0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2789563	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2789577	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2789578	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2818776	0.87[ASN][1000 genomes]
rs2818778	0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2818779	0.91[ASN][1000 genomes]
rs2818780	0.87[ASN][1000 genomes]
rs2818781	0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2818782	0.87[ASN][1000 genomes]
rs2818783	0.86[ASN][1000 genomes]
rs2818784	0.87[ASN][1000 genomes]
rs2818785	0.87[ASN][1000 genomes]
rs2818786	0.87[ASN][1000 genomes]
rs2818788	0.87[ASN][1000 genomes]
rs34247036	0.81[EUR][1000 genomes]
rs5017053	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6657447	0.88[ASN][1000 genomes]
rs6698252	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6698256	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7517404	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs7520445	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7526109	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1339219	SPATA17	cis	cerebellum	SCAN
rs1339219	LQK1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217157400-217194400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:217170800-217173600	Weak transcription	Left Ventricle	heart

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