Variant report

Variant	rs3812054
Chromosome Location	chr5:126732427-126732428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126732318..126732969-chr5:126828411..126828936,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10519929	1.00[CHD][hapmap]
rs10519930	1.00[CHD][hapmap]
rs10519937	0.82[EUR][1000 genomes]
rs10519938	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs11949373	0.87[EUR][1000 genomes]
rs11950058	0.87[EUR][1000 genomes]
rs11952947	0.87[EUR][1000 genomes]
rs11953024	0.87[EUR][1000 genomes]
rs11958435	0.87[EUR][1000 genomes]
rs11959505	0.84[EUR][1000 genomes]
rs1363385	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs1529467	0.87[EUR][1000 genomes]
rs17164935	0.84[CEU][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap]
rs17164979	0.87[EUR][1000 genomes]
rs17164995	0.84[CEU][hapmap]
rs17164996	0.84[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs17165035	0.83[CHD][hapmap]
rs17165082	0.85[CHD][hapmap]
rs17165105	1.00[CHD][hapmap]
rs173509	0.85[EUR][1000 genomes]
rs17444885	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604615	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604665	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604882	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17604889	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604946	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17673474	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673517	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17673685	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17763722	1.00[CHD][hapmap]
rs17839695	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs17839697	1.00[CHD][hapmap]
rs2068168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812053	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812055	0.84[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs41298308	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41298312	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563674	0.87[EUR][1000 genomes]
rs6595764	0.82[EUR][1000 genomes]
rs6595767	0.84[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs6595768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595769	0.84[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs67200948	0.86[EUR][1000 genomes]
rs67854568	0.87[EUR][1000 genomes]
rs68035691	0.87[EUR][1000 genomes]
rs6874392	0.87[EUR][1000 genomes]
rs6874521	0.84[CEU][hapmap]
rs6882034	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6888010	0.82[EUR][1000 genomes]
rs6891785	0.87[EUR][1000 genomes]
rs6892742	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6897290	0.84[EUR][1000 genomes]
rs72788576	0.86[ASN][1000 genomes]
rs72788578	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72788581	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790405	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790408	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790410	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790411	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790412	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790417	1.00[ASN][1000 genomes]
rs72790418	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790419	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790428	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790430	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790433	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790438	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790443	0.81[EUR][1000 genomes]
rs72790444	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790451	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790460	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790468	0.80[EUR][1000 genomes]
rs72790470	0.80[EUR][1000 genomes]
rs72790475	0.80[EUR][1000 genomes]
rs73786108	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7731380	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv526333	chr5:126732427-126746277	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3812054	SLC12A2	cis	cerebellum	SCAN
rs3812054	PRRC1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126691000-126746000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:126710200-126741200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:126712800-126734200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:126720000-126742000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:126722800-126736000	Weak transcription	HSMM	muscle
6	chr5:126729400-126732600	Weak transcription	Brain Angular Gyrus	brain
7	chr5:126730800-126734400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:126731000-126734400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:126731600-126732800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:126731600-126733800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:126731600-126735000	Enhancers	Brain Hippocampus Middle	brain
12	chr5:126731800-126733000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:126731800-126733000	Strong transcription	Fetal Muscle Leg	muscle
14	chr5:126731800-126735000	Genic enhancers	Brain Substantia Nigra	brain
15	chr5:126731800-126741800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:126731800-126742000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:126732000-126734400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:126732000-126735200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:126732000-126741200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:126732200-126732800	Strong transcription	HSMMtube	muscle
21	chr5:126732400-126732600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr5:126732400-126732800	Genic enhancers	Brain Anterior Caudate	brain
23	chr5:126732400-126734200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:126732400-126734800	Enhancers	Brain Cingulate Gyrus	brain
25	chr5:126732400-126741600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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