Variant report

Variant	rs10242061
Chromosome Location	chr7:39294042-39294043
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	chr7:39289451..39291797-chr7:39293526..39296522,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10263259	0.85[CHD][hapmap]
rs10265739	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10272803	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10951598	0.83[ASN][1000 genomes]
rs11505524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11771925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667875	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667891	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12672115	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28408659	0.83[ASN][1000 genomes]
rs28599716	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs35439815	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236356	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs4291171	0.85[ASN][1000 genomes]
rs4323393	0.82[CHB][hapmap]
rs4410807	0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4442033	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs4478468	0.82[CHD][hapmap]
rs4574755	0.84[JPT][hapmap]
rs4723832	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62453435	0.84[ASN][1000 genomes]
rs6956858	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs6958617	0.85[ASN][1000 genomes]
rs6962811	0.84[ASN][1000 genomes]
rs6974432	0.95[JPT][hapmap]
rs6974806	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs6974992	0.95[JPT][hapmap]
rs7777684	0.91[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs7789406	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7789925	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9655034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1015572	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv538821	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv887969	chr7:39265429-39391875	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10242061	TARP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39288800-39298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:39288800-39298200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:39289000-39297000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:39292800-39298000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:39293000-39294400	Weak transcription	Fetal Stomach	stomach
6	chr7:39293000-39298000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:39293000-39298200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:39293000-39298400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:39293000-39299800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:39293600-39298600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:39293800-39298200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:39293800-39310600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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