Variant report

Variant	rs6428843
Chromosome Location	chr1:120344398-120344399
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	chr1:120325629..120327668-chr1:120343274..120344889,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10494231	0.82[CEU][hapmap]
rs1052972	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs10737758	0.80[EUR][1000 genomes]
rs10737759	0.80[EUR][1000 genomes]
rs10737760	0.80[EUR][1000 genomes]
rs10754420	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs10754421	0.81[CEU][hapmap]
rs10754422	0.80[EUR][1000 genomes]
rs10754424	0.81[EUR][1000 genomes]
rs10802134	0.85[CEU][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs10802135	0.80[EUR][1000 genomes]
rs10802136	0.80[EUR][1000 genomes]
rs10802137	0.81[EUR][1000 genomes]
rs10923902	0.81[ASN][1000 genomes]
rs12047532	0.81[EUR][1000 genomes]
rs12730035	0.81[EUR][1000 genomes]
rs12747679	0.81[EUR][1000 genomes]
rs1441006	0.80[EUR][1000 genomes]
rs1441012	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1441013	0.81[EUR][1000 genomes]
rs1530227	0.80[EUR][1000 genomes]
rs1539071	0.81[EUR][1000 genomes]
rs1539074	0.81[EUR][1000 genomes]
rs1539075	0.81[EUR][1000 genomes]
rs17258467	0.80[EUR][1000 genomes]
rs2119470	0.81[EUR][1000 genomes]
rs2282403	1.00[ASW][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2289458	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2793836	0.85[CEU][hapmap]
rs4659236	0.80[EUR][1000 genomes]
rs4659237	0.81[EUR][1000 genomes]
rs6428841	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6428842	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6661517	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6683871	0.81[EUR][1000 genomes]
rs6698813	0.80[EUR][1000 genomes]
rs6698907	0.81[EUR][1000 genomes]
rs699778	0.85[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs7516324	0.81[EUR][1000 genomes]
rs935056	0.80[EUR][1000 genomes]
rs935057	0.80[EUR][1000 genomes]
rs935059	0.80[EUR][1000 genomes]
rs947270	0.85[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs947271	0.85[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6428843	SPAG17	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120336000-120349400	Weak transcription	Right Atrium	heart
2	chr1:120340600-120348000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:120340800-120351200	Weak transcription	Fetal Intestine Large	intestine
4	chr1:120342800-120351800	Weak transcription	Fetal Kidney	kidney
5	chr1:120343400-120344800	Weak transcription	Fetal Stomach	stomach
6	chr1:120344200-120344400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:120344200-120346400	Weak transcription	Pancreas	Pancrea

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