Variant report

Variant	rs10104767
Chromosome Location	chr8:50539763-50539764
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:50533493..50536467-chr8:50538326..50540996,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10098245	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10098599	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10099915	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11787471	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12056923	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1318749	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13250092	1.00[AMR][1000 genomes]
rs13277253	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13278513	1.00[AMR][1000 genomes]
rs13282371	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13282682	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1496313	1.00[ASN][1000 genomes]
rs1496314	1.00[ASN][1000 genomes]
rs1496315	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603399	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16910533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910609	1.00[ASN][1000 genomes]
rs1715339	0.86[EUR][1000 genomes]
rs1908709	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132527	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2173005	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28476719	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4455843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56269115	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57417954	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57583106	1.00[ASN][1000 genomes]
rs59722152	0.93[EUR][1000 genomes]
rs59759350	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60998432	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6472559	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6472567	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6472720	0.92[CHD][hapmap]
rs6472723	0.92[CHD][hapmap]
rs6996205	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6996381	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7002403	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73570804	0.86[EUR][1000 genomes]
rs73570889	0.93[EUR][1000 genomes]
rs73572931	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73572934	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73572942	0.86[EUR][1000 genomes]
rs73575139	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73679586	0.86[EUR][1000 genomes]
rs7387296	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7464002	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7825182	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825327	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825977	0.83[EUR][1000 genomes]
rs7845598	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917031	chr8:50207246-50709286	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2757271	chr8:50415233-50592704	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2759612	chr8:50415233-50657352	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv34838	chr8:50415247-50547507	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1023556	chr8:50415849-50559006	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv539602	chr8:50415849-50559006	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2758157	chr8:50415863-50657352	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv890862	chr8:50416266-50542665	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv890863	chr8:50430756-50639293	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv824622	chr8:50431222-50541803	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv890864	chr8:50435148-50542665	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1024890	chr8:50437965-50541405	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv539603	chr8:50437965-50541405	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv890868	chr8:50469764-50542665	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv890869	chr8:50469764-50558739	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv611310	chr8:50481632-50540708	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10104767	PRDX2	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50535600-50542800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:50537400-50541200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:50537600-50540000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr8:50537600-50540200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr8:50538200-50539800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr8:50538200-50540200	Enhancers	HMEC	breast
7	chr8:50538200-50540400	Enhancers	Fetal Lung	lung
8	chr8:50538400-50540400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:50538400-50540600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:50538800-50543000	Weak transcription	Ovary	ovary
11	chr8:50538800-50545000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr8:50539000-50540200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:50539200-50539800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr8:50539200-50539800	Enhancers	Fetal Kidney	kidney
15	chr8:50539200-50540000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr8:50539400-50539800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:50539400-50539800	Enhancers	Adipose Nuclei	Adipose
18	chr8:50539600-50539800	Enhancers	Skeletal Muscle Female	skeletal muscle

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