Variant report

Variant	rs16872517
Chromosome Location	chr7:108015724-108015725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108013080..108015754-chr7:108065360..108068339,2	MCF-7	breast:
2	chr7:108008768..108011253-chr7:108015718..108019224,4	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12534519	0.95[AMR][1000 genomes]
rs12537209	0.95[AMR][1000 genomes]
rs16872497	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16872512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872515	0.91[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17155397	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes]
rs17155405	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes]
rs17155446	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes]
rs17155536	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17155579	0.82[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs17155592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17155613	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17155617	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17329871	1.00[CEU][hapmap]
rs17330779	1.00[CEU][hapmap]
rs17388677	1.00[CEU][hapmap]
rs17388872	1.00[CEU][hapmap]
rs17420235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024491	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2193243	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2300020	0.95[AMR][1000 genomes]
rs2300031	0.87[ASN][1000 genomes]
rs55660243	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56100765	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59164222	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61657144	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6944131	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73420238	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73714833	0.87[ASN][1000 genomes]
rs73714837	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7792869	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7794233	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7811595	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes]
rs7812138	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108004000-108016600	Weak transcription	Pancreas	Pancrea
2	chr7:108004400-108016600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:108009400-108016600	Weak transcription	Brain Angular Gyrus	brain
4	chr7:108011800-108015800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:108012800-108021000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:108014000-108023400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:108014200-108016800	Weak transcription	A549	lung
8	chr7:108014800-108043200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:108015000-108017000	Enhancers	GM12878-XiMat	blood
10	chr7:108015400-108015800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:108015600-108015800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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