Variant report

Variant	rs7915926
Chromosome Location	chr10:99054052-99054053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr10:99053980-99054178	MCF10A-Er-Src	breast:	n/a	n/a
2	ARID3A	chr10:99053811-99054111	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99052581..99054143-chr10:99054832..99057681,2	K562	blood:
2	chr10:99050343..99055587-chr10:99077475..99082102,7	MCF-7	breast:
3	chr10:99051058..99054984-chr10:99078319..99082092,7	MCF-7	breast:
4	chr10:99051582..99055310-chr10:99077169..99083058,6	K562	blood:
5	chr10:99051582..99054067-chr10:99077169..99079188,3	K562	blood:

No data

Variant related genes	Relation type
ARHGAP19-SLIT1	TF binding region
ARHGAP19	TF binding region
ENSG00000165879	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1088187	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189121	0.90[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12240590	0.90[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1253386	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1253387	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1253396	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253397	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253400	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253401	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12769073	0.86[EUR][1000 genomes]
rs12782676	0.89[EUR][1000 genomes]
rs13439	0.90[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs2297987	0.80[TSI][hapmap]
rs2484880	0.89[CEU][hapmap]
rs2861877	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992773	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34115590	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34288920	0.88[EUR][1000 genomes]
rs34624597	0.89[EUR][1000 genomes]
rs36098270	0.88[EUR][1000 genomes]
rs4917765	0.87[EUR][1000 genomes]
rs61569149	0.82[EUR][1000 genomes]
rs61861842	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61861843	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61861844	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61861849	0.86[EUR][1000 genomes]
rs61861850	0.89[EUR][1000 genomes]
rs701821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs7074896	0.86[EUR][1000 genomes]
rs7091162	0.86[EUR][1000 genomes]
rs7101333	0.87[EUR][1000 genomes]
rs793515	0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs793516	0.85[CEU][hapmap]
rs793517	0.85[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs793519	0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs793520	0.90[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs793522	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793524	0.90[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs793531	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796980	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs946981	0.90[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]

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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription 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	27 gene(s)	inside rSNPs	diseases
5	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv7507	chr10:99031233-99070690	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv975787	chr10:99048466-99061224	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7915926	HELLS	cis	parietal	SCAN
rs7915926	RRP12	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99052000-99057600	Weak transcription	Fetal Heart	heart
2	chr10:99052400-99063800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:99052600-99054400	Enhancers	Liver	Liver
4	chr10:99052600-99061800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:99052800-99054400	Enhancers	Fetal Intestine Small	intestine
6	chr10:99052800-99054600	Enhancers	K562	blood
7	chr10:99052800-99057000	Weak transcription	A549	lung
8	chr10:99052800-99057600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:99052800-99057600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr10:99053400-99057000	Weak transcription	Fetal Intestine Large	intestine
11	chr10:99053400-99061000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:99053800-99054600	Enhancers	HepG2	liver

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