Variant report

Variant	rs462366
Chromosome Location	chr5:40821324-40821325
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	chr5:40776942..40778546-chr5:40820934..40823314,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10060234	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs1070446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155724	0.90[CEU][hapmap]
rs13167906	0.90[CEU][hapmap]
rs154268	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap]
rs154275	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs171605	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs173620	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs249414	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs249422	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs249425	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs249428	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs249429	0.85[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[YRI][hapmap]
rs249437	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs249441	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs257009	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs29742	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs29743	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs29744	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs29761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376831	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs381471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389737	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434778	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs4383756	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs447810	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs457776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461404	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.92[YRI][hapmap]
rs466108	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6451535	0.90[JPT][hapmap]
rs6897470	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7711806	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs7724201	0.80[EUR][1000 genomes]
rs7726237	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs837101	0.85[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
3	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs462366	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs462366		cis	Lymphoblastoid	GTEx
rs462366	RPL37	cis	cerebellum	SCAN
rs462366	FBXO4	cis	parietal	SCAN
rs462366	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs462366	RPL37	cis	parietal	SCAN
rs462366	RPL37,SNORD72	cis	brain	BrainEAC

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40808400-40826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:40808800-40825600	Weak transcription	HSMM	muscle
3	chr5:40813200-40823600	Weak transcription	K562	blood
4	chr5:40814000-40821600	Weak transcription	Thymus	Thymus
5	chr5:40814200-40826000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:40814200-40826000	Weak transcription	GM12878-XiMat	blood
7	chr5:40814200-40826400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:40814400-40825000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:40814400-40825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:40814600-40827000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:40816600-40826600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:40816600-40826800	Weak transcription	Brain Angular Gyrus	brain
13	chr5:40817400-40821600	Weak transcription	Fetal Thymus	thymus
14	chr5:40818600-40826600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:40818600-40827000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:40818800-40825200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:40818800-40826200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:40819000-40825200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:40819000-40825600	Weak transcription	NH-A	brain
20	chr5:40819000-40825600	Weak transcription	NHLF	lung
21	chr5:40819400-40826600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:40819600-40826600	Weak transcription	Primary B cells from cord blood	blood
23	chr5:40820000-40826400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:40820000-40826600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:40820000-40826800	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:40820200-40825600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:40820400-40825600	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:40820400-40827400	Weak transcription	Brain Substantia Nigra	brain
29	chr5:40820600-40824800	Weak transcription	Brain Germinal Matrix	brain
30	chr5:40820800-40822400	Weak transcription	Primary T cells from cord blood	blood
31	chr5:40820800-40825200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:40820800-40825400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:40821000-40827400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:40821200-40822600	Strong transcription	Fetal Brain Female	brain
35	chr5:40821200-40825600	Weak transcription	Brain Inferior Temporal Lobe	brain

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