Variant report

Variant	rs10245257
Chromosome Location	chr7:103278471-103278472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:103254361..103256762-chr7:103277435..103279324,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10244159	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10247439	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs11983439	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs123712	0.88[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs123713	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs123714	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12667604	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2058378	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2058379	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2073551	0.81[CEU][hapmap];0.80[AFR][1000 genomes]
rs2109697	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2159676	0.80[TSI][hapmap]
rs2159677	0.81[CEU][hapmap]
rs2191702	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237631	0.80[JPT][hapmap]
rs2245617	0.81[TSI][hapmap]
rs2249372	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299355	0.80[JPT][hapmap]
rs2535755	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2907929	0.84[ASN][1000 genomes]
rs362635	0.81[CEU][hapmap]
rs362642	0.81[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs362644	0.83[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs362658	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs362688	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs362695	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3757744	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3808024	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823981	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs496907	0.83[JPT][hapmap]
rs722613	0.94[JPT][hapmap]
rs9656083	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs995450	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831085	chr7:103140672-103342388	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv427799	chr7:103250733-103454202	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1835816	chr7:103255144-103354223	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv516122	chr7:103274567-103291825	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10245257	C7orf52	cis	parietal	SCAN
rs10245257	PRKAR2B	cis	cerebellum	SCAN
rs10245257	ZKSCAN5	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103273000-103283600	Weak transcription	K562	blood
2	chr7:103276600-103278800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:103276600-103279200	Enhancers	HMEC	breast
4	chr7:103276800-103279000	Enhancers	NH-A	brain
5	chr7:103276800-103279000	Enhancers	NHLF	lung
6	chr7:103276800-103279200	Enhancers	Osteobl	bone
7	chr7:103277000-103278800	Enhancers	NHEK	skin
8	chr7:103277000-103279000	Enhancers	Hela-S3	cervix
9	chr7:103277000-103279000	Enhancers	HUVEC	blood vessel
10	chr7:103277000-103281200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:103277000-103281200	Enhancers	NHDF-Ad	bronchial
12	chr7:103277000-103289200	Weak transcription	HepG2	liver
13	chr7:103277200-103278600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:103277400-103278800	Enhancers	HSMM	muscle
15	chr7:103277600-103279600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:103277600-103281400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:103278200-103278600	Enhancers	Muscle Satellite Cultured Cells	--

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